Compositions and methods for promoting the generation of definitive endoderm

ABSTRACT

Certain embodiments disclosed herein are directed to a method of producing endoderm cells, such as definitive endoderm cells by exposing stem cells such as embryonic stem cells or induced pluripotent stem (iPS) cells to an effective amount of at least one compound described herein to differentiate the stem cells into the endoderm cells such as definitive endoderm cells. Differentated endoderm cells produced by the methods disclosed herein can be differentiated into pancreatic epithelium, and other endoderm derivatives such as thymus, liver, stomach, intestine and lung. Another aspect of the present invention relates to a method of producing pancreatic progenitor cells, such as Pdx1-positive pancreatic progenitor cells by exposing endoderm cells, such as definitive endoderm cells to an effective amount of at least one compound described herein to differentiate the definitive endoderm cells into Pdx1-positive pancreatic progenitor cells. Kits and compositions comprising Pdx1-positive pancreatic progenitor produced using the methods are also described.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a 35 U.S.C. §371 National Stage Application ofInternational Application No. PCT/US2010/023303 filed on Feb. 5, 2010,which designates the United States, and which claims the benefit under35 U.S.C. §119(e) of U.S. Provisional Application Serial No: 61/150,509filed Feb. 6, 2009, the contents of which are incorporated herein byreference in its entirety.

GOVERNMENT SUPPORT

This invention was made with government support under DK072473 awardedby the National Institutes of Health. The government has certain rightsin the invention

FIELD OF THE INVENTION

Certain embodiments disclosed herein relate generally to stem cells.More particularly, certain examples disclosed herein relate topancreatic cells and pancreatic cell precursors that are produced byexposure of pluripotent stem cells, (e.g. human embryonic stem cells) oriPS cells, or endoderm cells (e.g. definitive endoderm cells) derivedtherefrom, to one or more small molecule compounds.

BACKGROUND OF THE INVENTION

Type I diabetes results from the destruction of insulin producingpancreatic beta cells and therefore there are several approaches aimedat cell-based strategies to replace these cells and rejuvenate thepancreas. The spontaneous or undirected differentiation of ES cellsproduces very small numbers of insulin producing cells, barely enoughfor research study and far short of the numbers needed for therapeuticapplication.

SUMMARY OF THE INVENTION

An essential step for therapeutic and research applications of stemcells is the ability to efficiently and reproducibly differentiate theminto specific differentiated cell types. Endodermal cell derivatives,including lung, liver and pancreas, are of interest for regenerativemedicine. The present invention generally describes herein features astrategy to increase the efficiency of beta cell formation by exposingstem cells, e.g. embryonic stem cells and derivatives to factors theywould normally encounter in vivo during embryonic development. Thestarting point for this strategy is differentiating stem cells, e.g.embryonic stem cells into definitive endoderm.

In particular, the present invention relates to methods and compositionsfor the efficient chemically mediated differentiation of pluripotentstem cells, such as embryonic stem cells and iPS cells, or variantsthereof into endoderm cells, in particular definitive endoderm cells. Insome embodiments, the method comprises contacting the pluripotent stemcells, such as embryonic stem cells and iPS cells with a compound ofFormula (I) as disclosed herein, such as a compound of IDE1 or IDE2 toinduce the differentiation of the pluripotent stem cells, such asembryonic stem cells and iPS cells to endoderm cells, in particulardefinitive endoderm cells. Such definitive endoderm cells are referredherein as chemically-induced definitive endoderm cells.

Another aspect relates to methods and compositions for the efficientdifferentiation of endoderm cells, such as definitive endoderm cellsinto pancreatic progenitor cells, which express Pdx1. In someembodiments, the method comprises contacting the definitive endodermcells with a compound of Formula (II) as disclosed herein, such as acompound of Indolactam V (ILV) to induce the differentiation of thedefinitive endoderm cells to pancreatic progenitor cells. Suchpancreatic progenitor cells are referred herein as chemically-inducedpancreatic progenitor cells.

Accordingly, the present invention provides an entirely chemicallymediated step-wise differentiation of preparing pancreatic progenitorcells from pluripotent stem cells, such as embryonic stem cells, iPScells or intermediates thereof. In particular, the present inventionprovides a two-stage approach for generating pancreatic progenitors frompluripotent stem cells, such as embryonic stem cells or iPS cells or thelike. In particular, Stage 1 contacting a population of pluripotent stemcells, such as embryonic stem cells or iPS cells with at least onecompound of Formula (I), such as IDE1 or IDE2 to generate endodermcells, such as definitive endoderm cells. In some embodiments, theendoderm cells, such as definitive endoderm cells from Stage 1 can beused in Stage 2. In some embodiments, Stage 2 comprises contacting apopulation of definitive endoderm cells with a compound of Formula (II),such as Indolactam V to generate Pdx1-positive pancreatic progenitorcells. In some embodiments, a further step (Step 3) can be performed ifthe user wants to obtain mature pancreatic islet cells or pancreaticβ-cells, by methods commonly known in the art, such as nicotinamide as aterminal differentiating agent, or transcription factors can beactivated by direct manipulation which causes progression from Pdx1positive pancreatic precursors to mature islet cells.

The step-wise approach to generate Pdx1-positive pancreatic precursorsfrom pluripotent stem cells is intended as a guide, and is not intendedto limit the invention except were explicitly indicated.

There have been several previous reports for the generation ofdefinitive endoderm cells, such as U.S. Pat. No. 7,510,876 which reportsusing growth factors of the TGFβ superfamily to differentiate humanpluripotent stem cells into definitive endoderm cells. However, unlikethe present invention, the '876 patent did not use chemical-mediateddifferentiation, nor did it report a compound of Formula (I), such asIDE1 or IDE2 to induce differentiation of pluripotent stem cells toendoderm cells. Furthermore, the '876 patent did not report a method toproduce pancreatic precursors from pluripotent stem cells in a two-stepprocess using only chemicals rather than growth factors, or geneticmanipulation of introducing transcription factors.

Similarly, while the U.S. Pat. No. 7,326,572 reports a method to produceendoderm cells from human embryonic cells, it reports a first step usinga combination of the growth factor Activin A with n-butyrate or thecombination of retinoic acid (RA) and enriching agents (e.g. seleniumand thyroid hormone, such as T3) to generate endoderm cells frompluripotent stem cells, and a second step of culturing the endodermcells with a combination of TGF-(antagonists such as Nogin, and mitogenssuch as FGF family members such as EGF) to generate Pdx1-positivepancreatic precursors from the endoderm cells, which can subsequently beused in a third step to differentiate the Pdx1-positive precursors intomature islet cells by nicotinamide or transcription factors to directthe progression from Pdx1 positive pancreatic precursors to mature isletcells. However, unlike the '572 application, which requires acombination of multiple different factors at each of the steps, thepresent invention only requires a cell to be contacted with a compoundof formula (I) (e.g. IDE1 or IDE2) in step 1 for chemically-inducing thedifferentiation of a pluripotent stem cell to an endoderm cell, such asdefinitive endoderm cell, and a compound of Formula (II) for step 2 tochemically-induce the differentiation of a definitive endoderm cell to aPdx1-positive pancreatic precursor cell.

In addition, other methods for producing definitive endoderm cells areknown in the art, including, for example the methods which are set forthin United States application publication US2006/0003446 to G. Keller, etal.; US2006/0003313 to K. D'Amour, et al., US2005/0158853 to K. D'Amour,et al., and US2005/0260749 of Jon Odorico, et al., relevant portions ofwhich are incorporated by reference herein. However, these reports donot teach or disclose methods for chemically-inducing thedifferentiation of pluripotent stem cells into endoderm cells, e.g.definitive endoderm cells, nor the use of compounds of Formula (I) (e.g.IDE1 or IDE2) for the chemical-induced differentiation of humanpluripotent stem cells into human endoderm cells, e.g. human definitiveendoderm cells. In some embodiments, the chemical-induceddifferentiation of human pluripotent stem cells into human endodermcells occurs by contacting the cells with a compound of Formula (I),e.g. IDE1 or IDE2 can include additional compounds, e.g. growth factorsor differentiation factors. Accordingly, the term “chemically-induced”as used herein does not preclude the use of additional factors incombination with a compound as disclosed herein. In some embodiments,“chemically-induced” refers to the use of the compounds alone for thechemically-mediated induced differentiation of a cell (e.g. of apluripotent stem cell into a definitive endoderm cell). In alternativeembodiments, “chemically-induced” refers to the use of the compounds(e.g. compounds of Formula (I) and/or Formula (II)) in the presence ofat least one additional agent (e.g. growth factors or other polypeptidesor small molecules) for the chemically-mediated induced differentiationof a cell (e.g. of a pluripotent stem cell into a definitive endodermcell)

In some embodiments, the definitive endoderm cells produced using themethods as described herein, e.g. by exposing pluripotent stem cells(e.g. embryonic stem cells or iPS cells) to at least one compound ofFormula (I) (e.g. IDE1 and/or IDE2) can, in addition to being used togenerate pancreatic epithelium (e.g. Pdx1-positive pancreatic progenitorcells), can also be used to generate other endoderm derivative cell suchas, but not limited to thymus, liver, stomach, intestine and lung.

One aspect of the present invention provides method of producing adefinitive endoderm cell from a pluripotent stem cell, where the methodscomprises contacting a population of pluripotent stem cells with atleast one compound of Formula (I) to induce the differentiation of atleast one pluripotent stem cell into a definitive endoderm cell, whereinthe definitive endoderm cell expresses Sox17, or HNF3B (FoxA2), or Sox17and HNF3B (FoxA2) and wherein the compound of formula (I) is:

wherein:

-   R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,    heteroaryl, cyclyl, or cyclyl, each of which can be optionally    substituted and/or can be interrupted in the backbone with one or    more of O, N, S, S(O), and C(O);-   R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl,    alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can be    optionally substituted, or R³ and R⁴ together with the carbon to    which they are attached from an optionally substituted cyclyl of    heterocycyl; and-   L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl,    each of which can be optionally substituted and/or can be    interrupted in the backbone with one or more of O, N, S, S(O), and    C(O).

In some embodiments, the pluripotent stem cell is an embryonic stem (ES)cell or an induced pluripotent stem (iPS) cell. In some embodiments, thestem cell is from a mammal, such as a human and the stem cell is a humanstem cell.

In some embodiments, the method further comprises isolating a populationof definitive endoderm cells, wherein at least 5%, 10%, 15%, 20%, 25%,30%, 35%, 50%, 75% or greater of the total cells in the isolatedpopulation are definitive endoderm cells.

In some embodiments of this and all aspect of the invention, a compoundof formula (I) is IDE1 having the structure:

In some embodiments of this and all aspect of the invention, a compoundof formula (I) is IDE2 having the structure:

In some embodiments of this and all aspect of the invention, a compoundof Formula (I) is an HDAC inhibitor.

In some embodiments of this and all aspect of the invention, apluripotent stem cell is contacted with the compound of Formula (I) forat least 1 day, for example, at least about 2 days, or at least about 3days, or at least about 3 days, or at least about 5 days, or at leastabout 6 days or more than 6 days.

In some embodiments, a pluripotent stem cell is contacted with acompound of Formula (I) at a concentration of between 25 nM-10 μM, forexample, in some embodiments, a pluripotent stem cell is contacted witha compound of Formula (I) which is IDE1 at a concentration of between 50nM-5 μM, or at a concentration of at least 50 nM, or at least 100 nM. Insome embodiments, a pluripotent stem cell is contacted with a compoundof Formula (I) which is IDE2 at a concentration of between 50 nM-5 μM,e.g. at a concentration of at least 100 nM or at least 200 nM.

In some embodiments, the at least 20% of the pluripotent stem cells inthe population of pluripotent stem cells are induced to differentiate adefinitive endoderm cell, and in some embodiments, at least 40% or atleast between 80-90% of the pluripotent stem cells in the population ofpluripotent stem cells are induced to differentiate a definitiveendoderm cell.

In some embodiments, the method for producing a definitive endoderm cellfrom a pluripotent stem cell comprising contacting a population ofpluripotent stem cells with at least one compound of Formula (I) toinduce the differentiation of at least one pluripotent stem cell into adefinitive endoderm cell, further comprising exposing the stem cells toat least one additional agent, e.g. an agent selected from the groupconsisting of: Nodal, Activin A or Wnt3a.

In some embodiments, a definitive endoderm cell produced by the methodsas disclosed herein expresses at least one marker selected from thegroup consisting of: Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2,Ripk4, Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnipl, Anxa4, Emb, FoxA1,Sox17, and Rbm35a, wherein the expression of at least one marker isupregulated to by a statistically significant amount in the definitiveendoderm cell relative to the pluripotent stem cell from which it wasderived. In some embodiments, a definitive endoderm cell produced by themethods as disclosed herein does not express by a statisticallysignificant amount at least one marker selected the group consisting of:Gata4, SPARC, AFP and Dab2 relative to the pluripotent stem cell fromwhich it was derived. In some embodiments, a definitive endoderm cellproduced by the methods as disclosed herein does not express by astatistically significant amount at least one marker selected the groupconsisting of: Zicl, Pax6, Flk1 and CD31 relative to the pluripotentstem cell from which it was derived.

In some embodiments, a definitive endoderm cell produced by the methodsas disclosed herein has a higher level of phosphorylation of Smad2 by astatistically significant amount relative to the pluripotent stem cellfrom which it was derived. In some embodiments, a definitive endodermcell produced by the methods as disclosed herein has the capacity toform gut tube in vivo. In some embodiments, a definitive endoderm cellproduced by the methods as disclosed herein can differentiate into acell with morphology characteristic of a gut cell, and wherein a cellwith morphology characteristic of a gut cell expresses FoxA2 and/orClaudin6. In some embodiments, a definitive endoderm cell produced bythe methods as disclosed herein can be further differentiated into acell of endoderm origin.

In some embodiments, the method for producing a definitive endoderm cellfrom a pluripotent stem cell comprising contacting a population ofpluripotent stem cells with at least one compound of Formula (I) toinduce the differentiation of at least one pluripotent stem cell into adefinitive endoderm cell, further comprises differentiating thedefinitive endoderm cell into a Pdx1-positive pancreatic progenitorcell, wherein the Pdx1-positive pancreatic progenitor cell expressesPdx1. In some embodiments, the Pdx1-positive pancreatic progenitor cellalso expresses HNF6.

In some embodiments, the method for producing a definitive endoderm cellfrom a pluripotent stem cell comprising contacting a population ofpluripotent stem cells with at least one compound of Formula (I) toinduce the differentiation of at least one pluripotent stem cell into adefinitive endoderm cell, further comprises contacting a population ofdefinitive endoderm cells with at least one compound of Formula (II) toinduce the differentiation of at least one definitive endoderm cell intoa Pdx1-positive pancreatic progenitor cell, wherein the compound offormula (II) is:

-   wherein: R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl,    cyclyl, or cyclyl, each of which can be optionally substituted;-   R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl,    alkynyl, alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which    can be optionally substituted; and-   R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl,    alkenyl, alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or    cyclyl, each of which can be optionally substituted, or R²⁴ and R²⁵    together with the carbons to which they are attached form an    optionally substituted cyclyl.

In all aspects and embodiments of the invention, a compound of Formula(II) is(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V).

In some embodiments, the methods for producing a population ofPdx1-positive pancreatic progenitor cells from definitive endoderm cell,where the definitive endoderm cells is chemically induced from apluripotent stem cell by contacting a population of pluripotent stemcells with at least one compound of Formula (I), which induces thedifferentiation of at least one pluripotent stem cell into a definitiveendoderm cell, and then the definitive endoderm cell further comprisescontacting a population of definitive endoderm cells with at least onecompound of Formula (II), the method can further comprise isolating thepopulation of Pdx1-positive pancreatic progenitor cells. In someembodiments, the method also further comprises differentiating thepopulation of Pdx1-positive pancreatic progenitor cells into apopulation of insulin producing cells, for example into a population ofcells having at least one characteristic of endogenous pancreaticβ-cells, or a cell with at least one characteristic of an endogenouspancreatic β-cell is secretion of insulin in response to glucose.

In some embodiments, the methods as disclosed herein for producingPdx1-positive pancreatic progenitors further comprises implanting apopulation of Pdx1-positive pancreatic progenitor cells or theirdifferentiated progeny of insulin producing cells or cells having atleast one characteristic of endogenous pancreatic β-cells into a subjectin need thereof. In some embodiments, the subject in need thereof hasdiabetes, or is at risk of developing diabetes. In some embodiments,where a definitive endoderm cell or a Pdx1-positive pancreaticprogenitor differentiated from said definitive endoderm cell is derivedfrom a pluripotent stem cell which is an iPS cell, the inducedpluripotent stem (iPS) cell can be obtained from a subject with diabetesor at risk of developing diabetes.

Another aspect of the present invention relates to an isolatedpopulation of definitive endoderm cells obtained from a population ofpluripotent stem cells by a process comprising contacting the populationof pluripotent stem cells with at least one compound of Formula (I),wherein the compound of Formula (I) is:

wherein:

-   R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,    heteroaryl, cyclyl, or cyclyl, each of which can be optionally    substituted and/or can be interrupted in the backbone with one or    more of O, N, S, S(O), and C(O);-   R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl,    alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can be    optionally substituted, or R³ and R⁴ together with the carbon to    which they are attached from an optionally substituted cyclyl of    heterocycyl; and-   L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl,    each of which can be optionally substituted and/or can be    interrupted in the backbone with one or more of O, N, S, S(O), and    C(O).

In some embodiments, an isolated population of definitive endoderm cellsobtained from a population of pluripotent stem cells by a processcomprising contacting the population of pluripotent stem cells with atleast one compound of IDE1 or IDE2, wherein the compound of IDE1 havingthe structure:

and the compound of IDE2 having the structure:

Another aspect of the present invention provides to an isolatedpopulation of Pdx1-positive pancreatic progenitors obtained from apopulation of pluripotent stem cells by a process comprising, (i)contacting the population of pluripotent stem cells with at least onecompound of Formula (I), (e.g. but not limited to IDE1 and/or IDE2) toinduce the differentiation of at least one pluripotent stem cell intodefinitive endoderm cell, and; (ii) contacting at least one definitiveendoderm cell with at least one compound of Formula (II) (e.g. but notlimited to indolatam V) to induce the differentiation of at least onedefinitive endoderm cell into a Pdx1-positive progenitor cell.

In some embodiments, an isolated population of Pdx1-positive pancreaticprogenitors obtained from pluripotent stem cells is obtained bycontacting a population of pluripotent stem cells with a compound ofwherein the compound of Formula (I) to produce definitive endodermcells, where compound of Formula (I) is:

wherein:

-   R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,    heteroaryl, cyclyl, or cyclyl, each of which can be optionally    substituted and/or can be interrupted in the backbone with one or    more of O, N, S, S(O), and C(O);-   R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl,    alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can be    optionally substituted, or R³ and R⁴ together with the carbon to    which they are attached from an optionally substituted cyclyl of    heterocycyl; and-   L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl,    each of which can be optionally substituted and/or can be    interrupted in the backbone with one or more of O, N, S, S(O), and    C(O).

In some embodiments and all aspects described herein, a compound ofFormula (I) used in the production of an isolated population ofPdx1-positive pancreatic progenitors selected from IDE1 or IDE2, whereinthe compound of IDE1 having the structure:

and the compound of IDE2 having the structure:

In some embodiments and all aspects described herein, a compound ofFormula (II) used in the production of an isolated population ofPdx1-positive pancreatic progenitors has the structure of:

-   wherein: R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl,    cyclyl, or cyclyl, each of which can be optionally substituted;-   R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl,    alkynyl, alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which    can be optionally substituted; and-   R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl,    alkenyl, alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or    cyclyl, each of which can be optionally substituted, or R²⁴ and R²⁵    together with the carbons to which they arre attached form an    optionally substituted cyclyl.

In some embodiments and all aspects described herein, a compound ofFormula (II) used in the production of an isolated population ofPdx1-positive pancreatic progenitors is(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V).

Another aspect of the present invention provides a compositioncomprising a population of definitive endoderm cells produced accordingto the any of the methods as disclosed herein, e.g. contacting apopulation of pluripotent stem cells with at least one compound ofFormula (I) (e.g. but not limited to IDE1 and/or IDE2) to induce thedifferentiation of at least one pluripotent stem cell into a definitiveendoderm cell

Another aspect of the present invention provides a compositioncomprising a population of Pdx1-positive pancreatic progenitor cellsproduced according to any of the methods as disclosed herein, e.g.contacting a population of definitive endoderm cells with at least onecompound of Formula (II) (e.g. indotactam V), to induce thedifferentiation of the definitive endoderm cells into a Pdx1-positivepancreatic progenitor, or e.g. contacting a pluripotent stem cells withat least one compound of Formula (I) (e.g. but not limited to IDE1and/or IDE2) to induce the differentiation of at least one pluripotentstem cell into a definitive endoderm cell, and the subsequentlycontacting a definitive endoderm cell with at least one compound ofFormula (II) (e.g. indotactam V), to induce the differentiation of thedefinitive endoderm cell into a Pdx1-positive pancreatic progenitorcell.

Another aspect of the present invention provides a method for thetreatment of a subject with diabetes, the method comprisingadministering to a subject a composition comprising an isolatedpopulation of Pdx1-positive pancreatic progenitor cells produced by themethods as disclosed herein or a differentiated progeny of aPdx1-positive pancreatic progenitor cells produced by the method asdisclosed herein. In some embodiments, the Pdx1-positive pancreaticprogenitor cells are produced from a population of pluripotent stemcells obtained from the same subject as the Pdx1-positive pancreaticprogenitor cells are administered to. In some embodiments, aPdx1-positive pancreatic progenitor cells are produced from anpopulation of iPS cell, wherein the iPS cell is derived from a cellobtained from the same subject as the Pdx1-positive pancreaticprogenitor cells are administered to.

In some embodiments, a subject administered a composition comprising anisolated population of Pdx1-positive pancreatic progenitor cells has, orhas an increased risk of developing diabetes, such as, for example, TypeI diabetes, Type II diabetes, Type 1.5 diabetes and pre-diabetes. Insome embodiments, the subject has, or has increased risk of developing ametabolic disorder.

Another aspect of the present invention provides the use of an isolatedpopulation of definitive endoderm cells produced by the methods asdisclosed herein for differentiating into Pdx1-positive pancreaticprogenitors.

Another aspect of the present invention provides the use of an isolatedpopulation of definitive endoderm cells produced by the methods asdisclosed herein for differentiating into a cell of endoderm origin, forexample into a cell such as a liver cell, a epithelial cell, apancreatic cell, a pancreatic endoderm (PE) cell, a thymus cell, anintestine cell, a stomach cell, a thyroid cell and a lung cell.

Another aspect of the present invention provides the use of an isolatedpopulation of Pdx1-positive progenitors produced by the methods asdisclosed herein for administering to a subject in need thereof, suchas, for example, a subject who has, or who has an increased risk ofdeveloping diabetes, such as Type I diabetes, Type II diabetes, Type 1.5and pre-diabetes. In some embodiments, the subject has, or has increasedrisk of developing a metabolic disorder.

Another aspect of the present invention provides a kit comprising atleast one compound of Formula (I) as disclosed herein. In someembodiments, the kit comprises a compound of Formula (I) which isselected from IDE1 or IDE2, wherein the compound of IDE1 having thestructure:

and the compound of IDE2 having the structure:

In some embodiments, the kit further comprises at least one compound ofFormula (II) as disclosed herein. In some embodiments, a compound ofFormula (II) is(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V).

In some embodiments, the kit further comprises an isolated population ofpluripotent stem cells, for example as a control population ofpluripotent stem cells. In some embodiments, the kit further comprises acontrol cell population selected from the group of; an endoderm cellpopulation, a definitive endoderm cell population, a pluripotent cellpopulation, a Pdx1-positive pancreatic progenitor cell population. Insome embodiments, the kit further comprises at least one agent for thedetection of a marker for a definitive endoderm cell, wherein the markercan be selected from any of the group consisting of; Nodal, Tmprss2,Tmem30b, St14, Spink3, Sh3gl2, Ripk4, Rab15, Npnt, Clic6, Cldn8,Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Sox17, and Rbm35a. In someembodiments, the kit further comprises at least one agent for thedetection of a marker for a Pdx1-positive pancreatic progenitor, whereinthe marker can be selected from any of the group consisting of; Pdxl andHNF6.

Another aspect of the present invention provides a reaction admixturecomprising a definitive endoderm cell and at least one compound ofFormula (I), as disclosed herein. In some embodiments, the admixturecomprises a definitive endoderm cell and a compound of Formula (I) whichis selected from IDE1 or IDE2, wherein the compound of IDE1 having thestructure:

and the compound of IDE2 having the structure:

Another aspect of the present invention provides a reaction admixturecomprising a pluripotent stem cell, e.g. iPS cell or embryonic stem celland at least one compound of Formula (I), as disclosed herein. In someembodiments, the admixture comprises a pluripotent stem cell and acompound of Formula (I) which is selected from IDE1 or IDE2, herein thecompound of IDE1 having the structure:

and the compound of IDE2 having the structure:

In some embodiments, the reaction admixture comprises a definitiveendoderm cell which is a human definitive endoderm cell. In someembodiments, the reaction admixture comprises a pluripotent stem cellwhich is a human pluripotent stem cell.

Another aspect of the present invention provides a reaction admixturecomprising a Pdx1-positive progenitor cell and at least one compound ofFormula (II) as disclosed herein. In some embodiments, the reactionadmixture comprises a Pdx1-positive progenitor cell and compound ofFormula (II) which is(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V).

Another aspect of the present invention provides a reaction admixturecomprising a definitive endoderm cell and at least one compound ofFormula (II) as disclosed herein. In some embodiments, the reactionadmixture comprises a definitive endoderm cell and a compound of Formula(II) which is(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V).

In some embodiments, the reaction admixture comprises a definitiveendoderm cell which is a human definitive endoderm cell. In someembodiments, the reaction admixture comprises a Pdx1-positive progenitorcell is a human Pdx1-positive progenitor cell. In some embodiments,admixtures comprising a Pdx1-positive progenitor cell comprise aPdx1-progenitor cell which has been differentiated from a definitiveendoderm cell, wherein the definitive endoderm cell has differentiatedfrom a pluripotent stem cell by contacting the pluripotent stem cellwith a compound of Formula (I), as disclosed herein.

In some embodiments, a reaction admixture comprising a Pdx1-positiveprogenitor cell can further comprises at least one compound of Formula(I) as disclosed herein. In some embodiments, a reaction admixturecomprising a Pdx1-positive progenitor cell can further comprises atleast one compound of Formula (I) which is selected from IDE1 or IDE2,wherein the compound of IDE1 having the structure.

and the compound of IDE2 having the structure:

BRIEF DESCRIPTION OF THE DRAWINGS

Certain illustrative embodiments are described in more detail below withreference to the accompanying figures.

FIG. 1A-1B shows a high throughput screening. FIG. 1A shows a scheme ofdifferentiation into endoderm and evaluation of an endoderm reporterline. Treatment with either Activin A or Nodal induces endoderm in mouseES cell cultures and at day 6 of treatment 45% of total cells areSox17/dsRed double positive (data not shown). Every dsRed+ cell stainspositively for Sox17 antibody (data not shown). FIG. 1B shows anoverview of the identification of endoderm inducers from small moleculecollection. Out of >4000 screened compounds, 27 primary hits wereselected and further evaluated for specificity and toxicity. Markers fordefinitive endoderm (DE) and extra-embryonic endoderm (EE) were testedby Q-RT-PCR and immunohistochemistry and 2 compounds that induced highlevels of DE were identified. ≧3 s.d=more than 3 standard deviations.

FIG. 2A-2B shows two small molecule inducers of endoderm (IDE). FIG. 2Ashows the chemical structure of IDE1 and IDE2 that induce endoderm cellsfrom mouse ES cells. FIG. 2B shows dose response curves of Sox17expression (based on immunofluorescence) following treatment withcompound for 6 days. The EC₅₀ values and curve fitting were performedwith Graph Prism software. Data presented as mean±s.d. n=4

FIG. 3A-3D show time course of endoderm induction and synergy betweendifferent compound (IDE1, IDE2, Activin A) and growth factors (Wnt3a,Nodal). FIGS. 3A and 3B show the effect of IDE1 and IDE2, respectively,on the number of Sox17+ and total cells during 14 days of treatment isshown. Endoderm induction by IDE1 and IDE2 peaks at about day 6 and aslittle as 12 hrs treatment with either compound is sufficient to induceSox17 expression in ˜40% of the cells. FIG. 3C shows the effect ofActivin A treatment on the number of Sox17+ and total cells during 14days of treatment. Activin A induces significant but lower % of Sox17+cells compared to IDE1 or IDE2 at all tested time points. Cells wereanalysed at day 6 (for earlier time points) or 14 of culture. FIG. 3Dshows the combined effect of compounds and growth factors on Sox17expression. Co-treatment of mouse ES cells with IDE1 or IDE2 compounds,alone or combined (IDE1+IDE2), or in the presence of Wnt3a or Nodalgrowth factors (IDE1+Wnt3a, IDE1+Nodal, IDE2+Wnt3a, IDE2+Nodal). Nodalenables shortening of the treatment time and leads to the induction ofSox17 with a slightly high efficiency (55.6%) expression at day 4. Nosynergy was detected between IDE1 and IDE2 (IDE1+IDE2) or thecombination of either compound IDE1 or IDE2 with Wnt3a. Allquantifications were based on the percentage of cells stained by Sox17antibody out of total cell. Data presented as mean±s.d. n=4 experiments.

FIG. 4A-4B shows gene expression analysis of IDE1 or IDE2 chemicallyinduced endoderm cells. FIG. 4A shows expression of definitiveendodermal markers in Sox17+ cells induced by compound treatment orisolated form E7.5-8.0 embryos. Sox17/dsRed+ cells were sorted by FACSand expression of endoderm genes was analysed by Illumina microarray.Expression of “endoderm signature” genes normalized to the DMSO treatedmouse ES cells is shown. Out of 17 genes, only 2, Spink3 and Tmprss2(marked by *) were expressed at significantly higher levels (>2 foldchange) in Sox17+ cells isolated from E7.75 embryos (endoderm). Each barrepresents an average of 3 biological replicates and mean±s.d. is shownFIG. 4B. FIG. 4B shows scatter plots comparing the global geneexpression in Sox17/dsRed+populations sorted out from Sox17/dsRed E7.75embryos and derived either in vitro by treatment with IDE2 (day 6 oftreatment) (left panel) or with non-treated mouse ES cell cultures(right panel). The centre diagonal line in the middle visualizes theequivalent levels in gene expression; the two lines either side of thecentre diagonal line show two-fold change in gene expression levelsbetween both samples.

FIG. 5A-5B show the effect of IDE1 and IDE2 small molecule inducers ofendoderm activate TGF-β signaling. FIG. 5A shows analysis ofphosphorylation of Smad2 in lysates of ES cells treated with IDE1, IDE2,DMSO, Activin A or Nodal or in the presence of the ALK4/5/7 inhibitor,SB431542. Treatment with IDE1 or IDE2 leads to activation of the TGF-βpathway after 24 hrs, similar to either Nodal or Activin A treatment.Phosphorylation of Smad2 by either of the two compounds is significantlyattenuated in the presence of SB431542. FIG. 5B shows an increase inNodal expression after treatment with small molecules IDE2 or IDE1 orNodal. Relative expression over DMSO treatment is shown as a mean oftriplicate experiments±s.d.

FIG. 6A-6B show functional evaluation of IDE1 and IDE2 chemicallyderived endoderm. FIG. 6A shows a schematic of in vivo assay to assessthe functional potential of compound induced endoderm. Mouse ES cellstreated with chemical inducers incorporate into the developing host guttube. Cultures of mouse ES cell reporter lines expressing constitutiveYFP were differentiated into endoderm with IDE1 or IDE2, producing60-70% Sox17+ cells, then trypsinized and injected into the nascent gutlumen of E8.75 mouse embryos. Dashed line shows an approximate plane ofsection. FIG. 6B shows that after 24-30 hours ex vivo culture, mouseembryos were fixed, transversally sectioned and stained with antibodiesagainst FoxA2 and Cldn6 to detect gut epithelial cells and anti-YFPantibodies to visualize injected cells. IDE1 and IDE2 induced endodermalcells incorporate into gut tube and show expression of gut tube markers.In contrast, DMSO treated cells remain clustered in the gut tube lumen30 hrs after injection and do not incorporate into the gut epithelia norexpress gut tube markers.

FIG. 7 shows a schematic of the developmental potential of IDE11 andIDE2 chemically derived endoderm, showing that differentiation of mouseES cells into Pdx1+ pancreatic progenitors by treatment of IDE1 or IDE2.Endoderm cells are first derived through treatment with either IDE1 orIDE2 and then formation of pancreatic progenitors was monitored using aPdx1-GFP reporter line.

FIG. 8A-8B show the generation of Sox17-dsRed reporter mouse ES line.FIG. 8A shows a schematic of the gene targeting strategy used to targetthe dsRed variant (Shaner et al., 2004) dTomato to the mouse Sox17locus. Indicated are the targeting vector with exons as grey boxes, thewild type locus and the targeted locus after homologous recombination.EcoRV and HindIII digest were used for Southern blot analysis with anexternal probe and an internal probe to identify properly targeted EScell clones. FIG. 8B shows Southern blot analysis with an external 5′probe (upper panel) and a probe against the neomycin selection cassette(lower panel) to confirm that positive clones, parental untargeted cellline, AV3, and targeted Sox17 dsRed clones. The wild type allelemigrates at 10.1 kb and the targeted allele at 6.1 kb as identified withthe external southern probe. A neomycin cassette can be identified at6.1 kb with a neo probe.

DETAILED DESCRIPTION OF THE INVENTION

Described herein are methods for the generation of endoderm, e.g.,definitive endoderm, by exposing a stem cell to one or more compoundsdescribed such as, for example, small molecule compounds. The methodsdescribed herein include producing an endoderm (i.e., an endodermalcell) by exposing a stem cell (e.g., an embryonic stem (ES) cell or iPScell) to a compound described herein e.g., a compound of formula (I),such as IDE1 or IDE2, or an HDAC inhibitor (e.g., a class I/II HDACinhibitor). In some embodiments the endoderm is further differentiatedto a second cell type.

Also described herein are compositions comprising isolated populationsof definitive endoderm cells and compositions comprising isolatedpopulations of pancreatic progenitor cells (e.g., cells produced by themethods described herein). Compositions and kits comprising thecompounds and/or cells described herein (e.g., made by method describedherein) are also include in the description.

In particular, the present invention relates to methods and compositionsfor chemically-induced differentiation of pluripotent stem cells, suchas embryonic stem cells and iPS cells, or variants thereof, intoendoderm cells, in particular definitive endoderm cells. The definitiveendoderm cells can be differentiated into any cell of endoderm origin,or alternatively in other embodiments, the definitive endoderm cells canbe differentiated into Pdx1-positive pancreatic progenitors. In someembodiments, the method comprises contacting the pluripotent stem cells,such as embryonic stem cells and iPS cells with a compound of Formula(I) as disclosed herein, such as a compound of IDE1 or IDE2 to inducethe differentiation of the pluripotent stem cells, such as embryonicstem cells and iPS cells to endoderm cells, in particular definitiveendoderm cells. Such definitive endoderm cells are referred herein aschemically-induced definitive endoderm cells. In some embodiments, thedefinitive endoderm cells produced by the chemically-induceddifferentiation of pluripotent stem cells have the positive expressionfor at least one or more of the following markers; Sox17+, and FoxA2+(HNF3β), and have negative or a low level of expression of at least oneof the markers selected from the group of Gata4, SPARC, APF, and Dab.

Another aspect relates to methods and compositions for the efficientdifferentiation of endoderm cells, such as definitive endoderm cellsinto pancreatic progenitor cells, which express Pdx1. In someembodiments, the method comprises contacting the definitive endodermcells with a compound of Formula (II) as disclosed herein, such as acompound of Indolactam V to induce the differentiation of the definitiveendoderm cells to pancreatic progenitor cells. Such pancreaticprogenitor cells are referred herein as chemically-induced pancreaticprogenitor cells. In some embodiments, the Pdx1-positive pancreaticprogenitors produced by chemically-induced differentiation of endodermcells, such as definitive endoderm cells are positive for the expressionof Pdx1 and HFN6.

Accordingly, the present invention provides an entirelychemically-induced two-step differentiation method for obtaining anisolated population of pancreatic progenitor cells from a population ofpluripotent stem cells, such as embryonic stem cells, iPS cells orintermediates thereof. In particular, the present invention provides atwo-stage approach for generating pancreatic progenitors frompluripotent stem cells, such as embryonic stem cells or iPS cells or thelike. In particular, Stage 1 contacting a population of pluripotent stemcells, such as embryonic stem cells or iPS cells with at least onecompound of Formula (I), such as IDE1 or IDE2 to generate endodermcells, such as definitive endoderm cells. In some embodiments, theendoderm cells, such as definitive endoderm cells from Stage 1 can beused in Stage 2. In some embodiments, Stage 2 comprises contacting apopulation of definitive endoderm cells with a compound of Formula (II),such as Indolactam V to generate Pdx1-positive pancreatic progenitorcells. In some embodiments, a further step (Step 3) can be performed ifthe user wants to obtain mature pancreatic islets or pancreatic β-cells,by methods commonly known in the art, such as nicotinamide as a terminaldifferentiating agent, or transcription factors can be activated bydirect manipulation which causes progression from Pdx1 positivepancreatic precursors to mature islet cells.

The methods and compositions as disclosed herein have a greater orsimilar efficiency as using TGF-β family members such as Activin A andNodal for producing pancreatic progenitors from stem cells, yet thepresent invention has numerous advantages including decreased cost ofmaterials, temporal control of the differentiation and reduced risk ofinfection and contamination of the cell population with growth factors.The step-wise approach to generate Pdx1-positive pancreatic precursorsfrom pluripotent stem cells is intended as a guide, and is not intendedto limit the invention except were explicitly indicated.

There have been several previous reports for the generation ofdefinitive endoderm cells, such as U.S. Pat. No. 7,510,876 which reportsusing growth factors of the TGFβ superfamily to differentiate humanpluripotent stem cells into definitive endoderm cells. However, unlikethe present invention, the '876 patent did not use chemical-mediateddifferentiation, nor did it report a compound of Formula (I), such asIDE1 or IDE2 to induce differentiation of pluripotent stem cells toendoderm cells. Furthermore, the '876 patent did not report a method toproduce pancreatic precursors from pluripotent stem cells in a two-stepprocess using only chemicals rather than growth factors, or geneticmanipulation of introducing transcription factors.

Definitions

For convenience, certain terms employed herein, in the specification,examples and appended claims are collected here. Unless otherwisedefined, all technical and scientific terms used herein have the samemeaning as commonly understood by one of ordinary skill in the art towhich this invention belongs.

The term “differentiated cell” is meant any primary cell that is not, inits native form, pluripotent as that term is defined herein. Statedanother way, the term “differentiated cell” refers to a cell of a morespecialized cell type derived from a cell of a less specialized celltype (e.g., a stem cell such as an induced pluripotent stem cell) in acellular differentiation process. Without wishing to be limited totheory, a pluripotent stem cell in the course of normal ontogeny candifferentiate first to an endoderm cell that is capable of formingpancreas cells and other endoderm cell types. Further differentiation ofan endoderm cell leads to the pancreatic pathway, where ˜98% of thecells become exocrine, ductular, or matrix cells, and ˜2% becomeendocrine cells. Early endocrine cells are islet progenitors, which canthen differentiate further into insulin producing cells (e.g. functionalendocrine cells) which secrete insulin, glucagon, somatostatin, orpancreatic polypeptide. Endoderm cells can also be differentiate intoother cells of endodermal origin, e.g. lung, liver, intestine, thymusetc.

As used herein, the term “somatic cell” refers to are any cells formingthe body of an organism, as opposed to germline cells. In mammals,germline cells (also known as “gametes”) are the spermatozoa and ovawhich fuse during fertilization to produce a cell called a zygote, fromwhich the entire mammalian embryo develops. Every other cell type in themammalian body—apart from the sperm and ova, the cells from which theyare made (gametocytes) and undifferentiated stem cells—is a somaticcell: internal organs, skin, bones, blood, and connective tissue are allmade up of somatic cells. In some embodiments the somatic cell is a“non-embryonic somatic cell”, by which is meant a somatic cell that isnot present in or obtained from an embryo and does not result fromproliferation of such a cell in vitro. In some embodiments the somaticcell is an “adult somatic cell”, by which is meant a cell that ispresent in or obtained from an organism other than an embryo or a fetusor results from proliferation of such a cell in vitro.

As used herein, the term “adult cell” refers to a cell found throughoutthe body after embryonic development.

The term “endoderm cell” as used herein refers to a cell which is fromone of the three primary germ cell layers in the very early embryo (theother two germ cell layers are the mesoderm and ectoderm). The endodermis the innermost of the three layers. An endoderm cell differentiates togive rise first to the embryonic gut and then to the linings ofrespiratory and digestive tracts (e.g. the intestine), the liver and thepancreas.

The term “a cell of endoderm origin” as used herein refers to any cellwhich has developed of differentiated from an endoderm cell. Forexample, a cell of endoderm origin includes cells of the liver, lung,pancrease, thymus, intestine, stomach and thyroid. Without wishing to bebound by theory, liver and pancreas progenitors (also referred to aspancreatic progenitors) are develop from endoderm cells in the embryonicforegut. Shortly after their specification, liver and pancreasprogenitors rapidly acquire markedly different cellular functions andregenerative capacities. These changes are elicited by inductive signalsand genetic regulatory factors that are highly conserved amongvertebrates. Interest in the development and regeneration of the organshas been fueled by the intense need for hepatocytes and pancreatic βcells in the therapeutic treatment of liver failure and type I diabetes.Studies in diverse model organisms and humans have revealedevolutionarily conserved inductive signals and transcription factornetworks that elicit the differentiation of liver and pancreatic cellsand provide guidance for how to promote hepatocyte and β celldifferentiation from diverse stem and progenitor cell types.

The term “definitive endoderm” as used herein refers to a celldifferentiated from an endoderm cell and which can be differentiatedinto a pancreatic β-cell. A definitive endoderm cell expresses themarker Sox17. Other markers of definitive endoderm cells include, butare not limited to MIXL2, GATA4, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1,CMKOR1 and CRIP1. In particular, definitive endoderm cells hereinexpress Sox17 and in some embodiments Sox17 and HNF3B, and do notexpress significant levels of GATA4, SPARC, APF or DAB. Definitiveendoderm cells are not positive for the marker Pdx1 (e.g. they arePdx1-negative). Definitive endoderm cells have the capacity todifferentiate into cells including those of the liver, lung, pancreas,thymus, intestine, stomach and thyroid.

The term “pancreatic progenitor” or “pancreatic precursor” are usedinterchangeably herein and refer to a stem cell which is capable offorming any of; pancreatic endocrine cells, or pancreatic exocrine cellsor pancreatic duct cells.

The term “pdx1-positive pancreatic progenitor” as used herein refers toa cell which is a pancreatic endoderm (PE) cell which has the capacityto differentiate into insulin producing cells, such as pancreaticβ-cells. A Pdx1-positive pancreatic progenitor expresses the markerPdx1. Other markers include, but are not limited to Cdcp1, or Ptf1a, orHNF6 or NRx2.2.

The term “pancreatic endoderm” refers to a cell of endoderm origin whichis capable of differentiating into multiple pancreatic lineages,including pancreatic beta cells, but no longer has the capacity todifferentiate into non-pancreatic lineages.

The term “exocrine cell” as used herein refers to a cell of an exocrinegland, i.e. a gland that discharges its secretion via a duct. Inparticular embodiments, an exocrine cells refers to a pancreaticexocrine cell, which is a pancreatic cell that produces enzymes that aresecreted into the small intestine. These enzymes help digest food as itpasses through the gastrointestinal tract. Pancreatic exocrine cells arealso known as islets of Langerhans, that secrete two hormones, insulinand glucagon. A pancreatic exocrine cell can be one of several celltypes: alpha-2 cells (which produce the hormone glucagon); or β-cells(which manufacture the hormone insulin); and alpha-1 cells (whichproduce the regulatory agent somatostatin). Non-insulin producingexocrine cells as used herein refers to alpha-2 cells or alpha-1 cells.Note, the term pancreatic exocrine cells encompasses “pancreaticendocrine cells” which refer to a pancreatic cell that produces hormones(e.g., insulin (produced from β-cells) and glucagon (produced by alpha-2cells) that are secreted into the bloodstream.

As used herein, the term “insulin producing cell” refers to a celldifferentiated from a pancreatic progenitor which secretes insulin. Aninsulin producing cell includes pancreatic β-cells as that term isdescribed herein, as well as pancreatic β-like cells that synthesize(i.e., transcribe the insulin gene, translate the proinsulin mRNA, andmodify the proinsulin mRNA into the insulin protein), express (i.e.,manifest the phenotypic trait carried by the insulin gene), or secrete(release insulin into the extracellular space) insulin in a constitutiveor inducible manner. A population of insulin producing cells e.g.produced by differentiating definitive endoderm cells to pancreaticprogenitors and then subsequent differentiation into insulin producingcells according to the methods of the present invention can bepancreatic β-cells or β-like cells (e.g., cells that have at least twocharacteristics of an endogenous β-cell). The novelty of the presentcomposition and methods is not negated by the presence of cells in thepopulation that produce insulin naturally (e.g., beta cells). It is alsocontemplated that the population of insulin producing cells, e.g.produced by the methods as disclosed herein can comprise pancreaticβ-cells or pancreatic β-like cells, and can also contain non-insulinproducing cells (i.e. cells of β-cell like phenotype with the exceptionthey do not produce or secrete insulin).

As used herein, the term “endogenous β-cell” or endogenous “pancreaticβ-cell” refers to an insulin producing cell of the pancreas or a cell ofa pancreatic β-cell (beta cell) phenotype. The phenotype of a pancreaticβ-cell is well known by persons of ordinary skill in the art, andinclude, for example, secretion of insulin in response to an increase inglucose level, expression of markers such as c-peptide, PDX-1polypeptide and Glut 2, as well as distinct morphologicalcharacteristics such as organized in islets in pancreas in vivo, andtypically have small spindle like cells of about 9-15 μm diameter.

The term “pancreatic β-like cell” as used herein refers to as usedherein refers to a cell produced by the methods as disclosed hereinwhich expresses at least 15% of the amount of insulin expressed by anendogenous pancreatic beta-cell, or at least about 20% or at least about30%, or at least about 40%, or at least about 50%, or at least about60%, or at least about 70%, or at least about 80%, or at least about90%, or at least about 100% or greater than 100%, such as at least about1.5-fold, or at least about 2-fold, or at least about 2.5-fold, or atleast about 3-fold, or at least about 4-fold or at least about 5-fold ormore than about 5-fold the amount of the insulin secreted by anendogenous pancreatic bets-cell, or alternatively exhibits at least one,or at least two characteristics of an endogenous pancreatic beta-cell,for example, but not limited to, secretion of insulin in response toglucose, and expression of beta-cell markers, such as for example,c-peptide, Pdx1 and glut-2. In one embodiment, the pancreatic β-likecell is not an immortalized cell (e.g. proliferate indefinitely inculture). In one embodiment, the pancreatic β-like cell is not atransformed cell, e.g., a cell that exhibits a transformation property,such as growth in soft agar, or absence of contact inhibition.

The term “β-cell marker” refers to, without limitation, proteins,peptides, nucleic acids, polymorphism of proteins and nucleic acids,splice variants, fragments of proteins or nucleic acids, elements, andother analytes which are specifically expressed or present in pancreaticβ-cells. Exemplary β-cell markers include, but are not limited to,pancreatic and duodenal homeobox 1 (PDX-1) polypeptide, insulin,c-peptide, amylin, E-cadherin, Hnf3β, PCI/3, Beta2, Nkx2.2, Nkx6.1,GLUT2, PC2, ZnT-8, and those described in Zhang et al., Diabetes.50(10):2231-6 (2001). In some embodiment, the β-cell marker is a nuclear3-cell marker. In some embodiments, the β-cell marker is PDX-1 or PH3.

The term “non-insulin producing cell” as used herein is meant any cellof endoderm origin that does not naturally synthesize, express, orsecrete insulin constitutively or by induction. Thus, the term“non-insulin producing cells” as used herein excludes pancreatic betacells. Examples of non-insulin producing cells that can be used in themethods of the present invention include pancreatic non-beta cells, suchas amylase producing cells, acinar cells, cells of ductal adenocarcinomacell lines (e.g., CD18, CD11, and Capan-I cells (see Busik et al., 1997;Schaffert et al. 1997). Non-pancreatic cells of endoderm origin couldalso be used, for example, non-pancreatic stem cells and cells of otherendocrine or exocrine organs, including, for example, liver cells, tymuscells, thyroid cells, intestine cells, lung cells and pituitary cells.In some embodiments, the non-insulin producing endodermal cells can bemammalian cells or, even more specifically, human cells. Examples of thepresent method using mammalian pancreatic non-islet, pancreatic amylaseproducing cells, pancreatic acinar cells are provided herein.

The term “phenotype” refers to one or a number of total biologicalcharacteristics that define the cell or organism under a particular setof environmental conditions and factors, regardless of the actualgenotype.

The term “pluripotent” as used herein refers to a cell with thecapacity, under different conditions, to differentiate to more than onedifferentiated cell type, and preferably to differentiate to cell typescharacteristic of all three germ cell layers. Pluripotent cells arecharacterized primarily by their ability to differentiate to more thanone cell type, preferably to all three germ layers, using, for example,a nude mouse teratoma formation assay. Pluripotency is also evidenced bythe expression of embryonic stem (ES) cell markers, although thepreferred test for pluripotency is the demonstration of the capacity todifferentiate into cells of each of the three germ layers. It should benoted that simply culturing such cells does not, on its own, render thempluripotent. Reprogrammed pluripotent cells (e.g. iPS cells as that termis defined herein) also have the characteristic of the capacity ofextended passaging without loss of growth potential, relative to primarycell parents, which generally have capacity for only a limited number ofdivisions in culture.

As used herein, the terms “iPS cell” and “induced pluripotent stem cell”are used interchangeably and refers to a pluripotent stem cellartificially derived (e.g., induced or by complete reversal) from anon-pluripotent cell, typically an adult somatic cell, for example, byinducing a forced expression of one or more genes.

The term “progenitor” or “precursor” cell are used interchangeablyherein and refer to cells that have a cellular phenotype that is moreprimitive (i.e., is at an earlier step along a developmental pathway orprogression than is a fully differentiated cell) relative to a cellwhich it can give rise to by differentiation. Often, progenitor cellsalso have significant or very high proliferative potential. Progenitorcells can give rise to multiple distinct differentiated cell types or toa single differentiated cell type, depending on the developmentalpathway and on the environment in which the cells develop anddifferentiate.

The term “stem cell” as used herein, refers to an undifferentiated cellwhich is capable of proliferation and giving rise to more progenitorcells having the ability to generate a large number of mother cells thatcan in turn give rise to differentiated, or differentiable daughtercells. The daughter cells themselves can be induced to proliferate andproduce progeny that subsequently differentiate into one or more maturecell types, while also retaining one or more cells with parentaldevelopmental potential. The term “stem cell” refers to a subset ofprogenitors that have the capacity or potential, under particularcircumstances, to differentiate to a more specialized or differentiatedphenotype, and which retains the capacity, under certain circumstances,to proliferate without substantially differentiating. In one embodiment,the term stem cell refers generally to a naturally occurring mother cellwhose descendants (progeny) specialize, often in different directions,by differentiation, e.g., by acquiring completely individual characters,as occurs in progressive diversification of embryonic cells and tissues.Cellular differentiation is a complex process typically occurringthrough many cell divisions. A differentiated cell may derive from amultipotent cell which itself is derived from a multipotent cell, and soon. While each of these multipotent cells may be considered stem cells,the range of cell types each can give rise to may vary considerably.Some differentiated cells also have the capacity to give rise to cellsof greater developmental potential. Such capacity may be natural or maybe induced artificially upon treatment with various factors. In manybiological instances, stem cells are also “multipotent” because they canproduce progeny of more than one distinct cell type, but this is notrequired for “stem-ness.” Self-renewal is the other classical part ofthe stem cell definition, and it is essential as used in this document.In theory, self-renewal can occur by either of two major mechanisms.Stem cells may divide asymmetrically, with one daughter retaining thestem state and the other daughter expressing some distinct otherspecific function and phenotype. Alternatively, some of the stem cellsin a population can divide symmetrically into two stems, thusmaintaining some stem cells in the population as a whole, while othercells in the population give rise to differentiated progeny only.Formally, it is possible that cells that begin as stem cells mightproceed toward a differentiated phenotype, but then “reverse” andre-express the stem cell phenotype, a term often referred to as“dedifferentiation” or “reprogramming” or “retrodifferentiation” bypersons of ordinary skill in the art.

In the context of cell ontogeny, the adjective “differentiated”, or“differentiating” is a relative term meaning a “differentiated cell” isa cell that has progressed further down the developmental pathway thanthe cell it is being compared with. Thus, stem cells can differentiateto lineage-restricted precursor cells (such as a mesodermal stem cell),which in turn can differentiate into other types of precursor cellsfurther down the pathway (such as an cardiomyocyte precursor), and thento an end-stage differentiated cell, which plays a characteristic rolein a certain tissue type, and may or may not retain the capacity toproliferate further.

The term “embryonic stem cell” is used to refer to the pluripotent stemcells of the inner cell mass of the embryonic blastocyst (see U.S. Pat.Nos. 5,843,780, 6,200,806). Such cells can similarly be obtained fromthe inner cell mass of blastocysts derived from somatic cell nucleartransfer (see, for example, U.S. Pat. Nos. 5,945,577, 5,994,619,6,235,970). The distinguishing characteristics of an embryonic stem celldefine an embryonic stem cell phenotype. Accordingly, a cell has thephenotype of an embryonic stem cell if it possesses one or more of theunique characteristics of an embryonic stem cell such that that cell canbe distinguished from other cells. Exemplary distinguishing embryonicstem cell characteristics include, without limitation, gene expressionprofile, proliferative capacity, differentiation capacity, karyotype,responsiveness to particular culture conditions, and the like.

The term “adult stem cell” or “ASC” is used to refer to any multipotentstem cell derived from non-embryonic tissue, including fetal, juvenile,and adult tissue. Stem cells have been isolated from a wide variety ofadult tissues including blood, bone marrow, brain, olfactory epithelium,skin, pancreas, skeletal muscle, and cardiac muscle. Each of these stemcells can be characterized based on gene expression, factorresponsiveness, and morphology in culture. Exemplary adult stem cellsinclude neural stem cells, neural crest stem cells, mesenchymal stemcells, hematopoietic stem cells, and pancreatic stem cells. As indicatedabove, stem cells have been found resident in virtually every tissue.Accordingly, the present invention appreciates that stem cellpopulations can be isolated from virtually any animal tissue.

The term “pancreas” refers to a glandular organ that secretes digestiveenzymes and hormones. In humans, the pancreas is a yellowish organ about7 in. (17.8 cm) long and 1.5 in. (3.8 cm) wide. It lies beneath thestomach and is connected to the small intestine, muscular hoselikeportion of the gastrointestinal tract extending from the lower end ofthe stomach (pylorus) to the anal opening. Most of the pancreatic tissueconsists of grapelike clusters of cells that produce a clear fluid(pancreatic juice) that flows into the duodenum through a common ductalong with bile from the liver. Pancreatic juice contains threedigestive enzymes: tryptase, amylase, and lipase, that, along withintestinal enzymes, complete the digestion of proteins, carbohydrates,and fats, respectively. Scattered among the enzyme-producing cells ofthe pancreas are small groups of endocrine cells, called the islets ofLangerhans, that secrete two hormones, insulin and glucagon. Thepancreatic islets contain several types of cells: alpha-2 cells, whichproduce the hormone glucagon; beta cells (also referred to herein as“pancreatic β-cells”), which manufacture the hormone insulin; andalpha-1 cells, which produce the regulatory agent somatostatin. Thesehormones are secreted directly into the bloodstream, and together, theyregulate the level of glucose in the blood. Insulin lowers the bloodsugar level and increases the amount of glycogen (stored carbohydrate)in the liver; glucagon has the opposite action. Failure of theinsulin-secreting cells to function properly results in diabetes ordiabetes mellitus.

The term “reprogramming” as used herein refers to the process thatalters or reverses the differentiation state of a somatic cell. The cellcan either be partially or terminally differentiated prior to thereprogramming. Reprogramming encompasses complete reversion of thedifferentiation state of a somatic cell to a pluripotent cell. Suchcomplete reversal of differentiation produces an induced pluripotent(iPS) cell. Reprogramming as used herein also encompasses partialreversion of a cells differentiation state, for example to a multipotentstate or to a somatic cell that is neither pluripotent or multipotent,but is a cell that has lost one or more specific characteristics of thedifferentiated cell from which it arises, e.g. direct reprogramming of adifferentiated cell to a different somatic cell type. Reprogramminggenerally involves alteration, e.g., reversal, of at least some of theheritable patterns of nucleic acid modification (e.g., methylation),chromatin condensation, epigenetic changes, genomic imprinting, etc.,that occur during cellular differentiation as a zygote develops into anadult.

The term “agent” as used herein means any compound or substance such as,but not limited to, a small molecule, nucleic acid, polypeptide,peptide, drug, ion, etc. An “agent” can be any chemical, entity ormoiety, including without limitation synthetic and naturally-occurringproteinaceous and non-proteinaceous entities. In some embodiments, anagent is nucleic acid, nucleic acid analogues, proteins, antibodies,peptides, aptamers, oligomer of nucleic acids, amino acids, orcarbohydrates including without limitation proteins, oligonucleotides,ribozymes, DNAzymes, glycoproteins, siRNAs, lipoproteins, aptamers, andmodifications and combinations thereof etc. In certain embodiments,agents are small molecule having a chemical moiety. For example,chemical moieties included unsubstituted or substituted alkyl, aromatic,or heterocycyll moieties including macrolides, leptomycins and relatednatural products or analogues thereof. Compounds can be known to have adesired activity and/or property, or can be selected from a library ofdiverse compounds.

As used herein, the term “contacting” (i.e., contacting a pluripotentstem cell or a definitive endoderm cell, with a compound) is intended toinclude incubating the compound and the cell together in vitro (e.g.,adding the compound to cells in culture). In some embodiments, the term“contacting” is not intended to include the in vivo exposure of cells tothe compounds as disclosed herein that may occur naturally in a subject(i.e., exposure that may occur as a result of a natural physiologicalprocess). The step of contacting a pluripotent stem cell with a compoundof Formula (I) as in the embodiments related to the production ofdefinitive endoderm cells can be conducted in any suitable manner. Forexample, the cells may be treated in adherent culture, or in suspensionculture. It is understood that the cells contacted with a compound ofFormula (I) or of Formula (II) can also be simultaneously orsubsequently contacted with another agent, such as a growth factor orother differentiation agent or environments to stabilize the cells, orto differentiate the cells further. Similarly, a pluripotent stem cellcan be contacted with a compound of Formula (I) and then with a compoundof Formula (II). In some embodiments, the cell is contacted with acompound of Formula (I) and Formula (II) and the contact is temporalseparated, and in some embodiments, a cell is contacted with a compoundof Formula (I) and Formula (II) substantially simultaneously.

The term “cell culture medium” (also referred to herein as a “culturemedium” or “medium”) as referred to herein is a medium for culturingcells containing nutrients that maintain cell viability and supportproliferation. The cell culture medium may contain any of the followingin an appropriate combination: salt(s), buffer(s), amino acids, glucoseor other sugar(s), antibiotics, serum or serum replacement, and othercomponents such as peptide growth factors, etc. Cell culture mediaordinarily used for particular cell types are known to those skilled inthe art.

The term “cell line” refers to a population of largely or substantiallyidentical cells that has typically been derived from a single ancestorcell or from a defined and/or substantially identical population ofancestor cells. The cell line may have been or may be capable of beingmaintained in culture for an extended period (e.g., months, years, foran unlimited period of time). It may have undergone a spontaneous orinduced process of transformation conferring an unlimited culturelifespan on the cells. Cell lines include all those cell linesrecognized in the art as such. It will be appreciated that cells acquiremutations and possibly epigenetic changes over time such that at leastsome properties of individual cells of a cell line may differ withrespect to each other.

The term “exogenous” refers to a substance present in a cell or organismother than its native source. For example, the terms “exogenous nucleicacid” or “exogenous protein” refer to a nucleic acid or protein that hasbeen introduced by a process involving the hand of man into a biologicalsystem such as a cell or organism in which it is not normally found orin which it is found in lower amounts. A substance will be consideredexogenous if it is introduced into a cell or an ancestor of the cellthat inherits the substance. In contrast, the term “endogenous” refersto a substance that is native to the biological system.

The term “expression” refers to the cellular processes involved inproducing RNA and proteins and as appropriate, secreting proteins,including where applicable, but not limited to, for example,transcription, translation, folding, modification and processing.“Expression products” include RNA transcribed from a gene andpolypeptides obtained by translation of mRNA transcribed from a gene.

The term “genetically modified” or “engineered” cell as used hereinrefers to a cell into which an exogenous nucleic acid has beenintroduced by a process involving the hand of man (or a descendant ofsuch a cell that has inherited at least a portion of the nucleic acid).The nucleic acid may for example contain a sequence that is exogenous tothe cell, it may contain native sequences (i.e., sequences naturallyfound in the cells) but in a non-naturally occurring arrangement (e.g.,a coding region linked to a promoter from a different gene), or alteredversions of native sequences, etc. The process of transferring thenucleic into the cell can be achieved by any suitable technique.Suitable techniques include calcium phosphate or lipid-mediatedtransfection, electroporation, and transduction or infection using aviral vector. In some embodiments the polynucleotide or a portionthereof is integrated into the genome of the cell. The nucleic acid mayhave subsequently been removed or excised from the genome, provided thatsuch removal or excision results in a detectable alteration in the cellrelative to an unmodified but otherwise equivalent cell.

The term “identity” as used herein refers to the extent to which thesequence of two or more nucleic acids or polypeptides is the same. Thepercent identity between a sequence of interest and a second sequenceover a window of evaluation, e.g., over the length of the sequence ofinterest, may be computed by aligning the sequences, determining thenumber of residues (nucleotides or amino acids) within the window ofevaluation that are opposite an identical residue allowing theintroduction of gaps to maximize identity, dividing by the total numberof residues of the sequence of interest or the second sequence(whichever is greater) that fall within the window, and multiplying by100. When computing the number of identical residues needed to achieve aparticular percent identity, fractions are to be rounded to the nearestwhole number. Percent identity can be calculated with the use of avariety of computer programs known in the art. For example, computerprograms such as BLAST2, BLASTN, BLASTP, Gapped BLAST, etc., generatealignments and provide percent identity between sequences of interest.The algorithm of Karlin and Altschul (Karlin and Altschul, Proc. Natl.Acad. Sci. USA 87:22264-2268, 1990) modified as in Karlin and Altschul,Proc. Natl. Acad. ScL USA 90:5873-5877, 1993 is incorporated into theNBLAST and XBLAST programs of Altschul et al. (Altschul, et al., J. MoI.Biol. 215:403-410, 1990). To obtain gapped alignments for comparisonpurposes, Gapped BLAST is utilized as described in Altschul et al.(Altschul, et al. Nucleic Acids Res. 25: 3389-3402, 1997). Whenutilizing BLAST and Gapped BLAST programs, the default parameters of therespective programs may be used. A PAM250 or BLOSUM62 matrix may beused. Software for performing BLAST analyses is publicly availablethrough the National Center for Biotechnology Information (NCBI). Seethe Web site having URL world-wide web address of: “ncbi.nlm nih.gov”for these programs. In a specific embodiment, percent identity iscalculated using BLAST2 with default parameters as provided by the NCBI.

The term “isolated” or “partially purified” as used herein refers, inthe case of a nucleic acid or polypeptide, to a nucleic acid orpolypeptide separated from at least one other component (e.g., nucleicacid or polypeptide) that is present with the nucleic acid orpolypeptide as found in its natural source and/or that would be presentwith the nucleic acid or polypeptide when expressed by a cell, orsecreted in the case of secreted polypeptides. A chemically synthesizednucleic acid or polypeptide or one synthesized using in vitrotranscription/translation is considered “isolated”.

The term “isolated cell” as used herein refers to a cell that has beenremoved from an organism in which it was originally found or adescendant of such a cell. Optionally the cell has been cultured invitro, e.g., in the presence of other cells. Optionally the cell islater introduced into a second organism or re-introduced into theorganism from which it (or the cell from which it is descended) wasisolated.

The term “isolated population” with respect to an isolated population ofcells as used herein refers to a population of cells that has beenremoved and separated from a mixed or heterogeneous population of cells.In some embodiments, an isolated population is a substantially purepopulation of cells as compared to the heterogeneous population fromwhich the cells were isolated or enriched from.

The term “substantially pure”, with respect to a particular cellpopulation, refers to a population of cells that is at least about 75%,preferably at least about 85%, more preferably at least about 90%, andmost preferably at least about 95% pure, with respect to the cellsmaking up a total cell population. Recast, the terms “substantiallypure” or “essentially purified”, with regard to a population ofdefinitive endoderm cells, refers to a population of cells that containfewer than about 20%, more preferably fewer than about 15%, 10%, 8%, 7%,most preferably fewer than about 5%, 4%, 3%, 2%, 1%, or less than 1%, ofcells that are not definitive endoderm cells or their progeny as definedby the terms herein. In some embodiments, the present inventionencompasses methods to expand a population of definitive endoderm cells,wherein the expanded population of definitive endoderm cells is asubstantially pure population of definitive endoderm cells. Similarly,with regard to a “substantially pure” or “essentially purified”population of Pdx1-positive pancreatic progenitors, refers to apopulation of cells that contain fewer than about 20%, more preferablyfewer than about 15%, 10%, 8%, 7%, most preferably fewer than about 5%,4%, 3%, 2%, 1%, or less than 1%, of cells that are not Pdx1-positivepancreatic progenitors or their progeny as defined by the terms herein.In some embodiments, the present invention encompasses methods to expanda population of Pdx1-positive pancreatic progenitors, wherein theexpanded population of Pdx1-positive pancreatic progenitors is asubstantially pure population of Pdx1-positive pancreatic progenitors.

The terms “enriching” or “enriched” are used interchangeably herein andmean that the yield (fraction) of cells of one type is increased by atleast 10% over the fraction of cells of that type in the startingculture or preparation.

The terms “renewal” or “self-renewal” or “proliferation” are usedinterchangeably herein, are used to refer to the ability of stem cellsto renew themselves by dividing into the same non-specialized cell typeover long periods, and/or many months to years. In some instances,proliferation refers to the expansion of cells by the repeated divisionof single cells into two identical daughter cells.

The term “lineages” as used herein describes a cell with a commonancestry or cells with a common developmental fate. In the context of acell that is of endoderm origin or is “endodermal linage” this means thecell was derived from an endoderm cell and can differentiate along theendoderm lineage restricted pathways, such as one or more developmentallineage pathways which give rise to definitive endoderm cells, which inturn can differentiate into liver cells, thymus, pancreas, lung andintestine.

As used herein, the term “xenogeneic” refers to cells that are derivedfrom different species.

A “marker” as used herein is used to describe the characteristics and/orphenotype of a cell. Markers can be used for selection of cellscomprising characteristics of interests. Markers will vary with specificcells. Markers are characteristics, whether morphological, functional orbiochemical (enzymatic) characteristics of the cell of a particular celltype, or molecules expressed by the cell type. Preferably, such markersare proteins, and more preferably, possess an epitope for antibodies orother binding molecules available in the art. However, a marker mayconsist of any molecule found in a cell including, but not limited to,proteins (peptides and polypeptides), lipids, polysaccharides, nucleicacids and steroids. Examples of morphological characteristics or traitsinclude, but are not limited to, shape, size, and nuclear to cytoplasmicratio. Examples of functional characteristics or traits include, but arenot limited to, the ability to adhere to particular substrates, abilityto incorporate or exclude particular dyes, ability to migrate underparticular conditions, and the ability to differentiate along particularlineages. Markers may be detected by any method available to one ofskill in the art. Markers can also be the absence of a morphologicalcharacteristic or absence of proteins, lipids etc. Markers can be acombination of a panel of unique characteristics of the presence andabsence of polypeptides and other morphological characteristics.

The term “modulate” is used consistently with its use in the art, i.e.,meaning to cause or facilitate a qualitative or quantitative change,alteration, or modification in a process, pathway, or phenomenon ofinterest. Without limitation, such change may be an increase, decrease,or change in relative strength or activity of different components orbranches of the process, pathway, or phenomenon. A “modulator” is anagent that causes or facilitates a qualitative or quantitative change,alteration, or modification in a process, pathway, or phenomenon ofinterest.

As used herein, the term “DNA” is defined as deoxyribonucleic acid.

The term “polynucleotide” is used herein interchangeably with “nucleicacid” to indicate a polymer of nucleosides. Typically a polynucleotideof this invention is composed of nucleosides that are naturally found inDNA or RNA (e.g., adenosine, thymidine, guanosine, cytidine, uridine,deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine)joined by phosphodiester bonds. However the term encompasses moleculescomprising nucleosides or nucleoside analogs containing chemically orbiologically modified bases, modified backbones, etc., whether or notfound in naturally occurring nucleic acids, and such molecules may bepreferred for certain applications. Where this application refers to apolynucleotide it is understood that both DNA, RNA, and in each caseboth single- and double-stranded forms (and complements of eachsingle-stranded molecule) are provided. “Polynucleotide sequence” asused herein can refer to the polynucleotide material itself and/or tothe sequence information (i.e. the succession of letters used asabbreviations for bases) that biochemically characterizes a specificnucleic acid. A polynucleotide sequence presented herein is presented ina 5′ to 3′ direction unless otherwise indicated.

The terms “polypeptide” as used herein refers to a polymer of aminoacids. The terms “protein” and “polypeptide” are used interchangeablyherein. A peptide is a relatively short polypeptide, typically betweenabout 2 and 60 amino acids in length. Polypeptides used herein typicallycontain amino acids such as the 20 L-amino acids that are most commonlyfound in proteins. However, other amino acids and/or amino acid analogsknown in the art can be used. One or more of the amino acids in apolypeptide may be modified, for example, by the addition of a chemicalentity such as a carbohydrate group, a phosphate group, a fatty acidgroup, a linker for conjugation, functionalization, etc. A polypeptidethat has a non-polypeptide moiety covalently or non-covalentlyassociated therewith is still considered a “polypeptide”. Exemplarymodifications include glycosylation and palmitoylation. Polypeptides maybe purified from natural sources, produced using recombinant DNAtechnology, synthesized through chemical means such as conventionalsolid phase peptide synthesis, etc. The term “polypeptide sequence” or“amino acid sequence” as used herein can refer to the polypeptidematerial itself and/or to the sequence information (i.e., the successionof letters or three letter codes used as abbreviations for amino acidnames) that biochemically characterizes a polypeptide. A polypeptidesequence presented herein is presented in an N-terminal to C-terminaldirection unless otherwise indicated.

The term a “variant” in referring to a polypeptide could be, e.g., apolypeptide at least 80%, 85%, 90%, 95%, 98%, or 99% identical to fulllength polypeptide. The variant could be a fragment of full lengthpolypeptide The variant could be a naturally occurring splice variant.The variant could be a polypeptide at least 80%, 85%, 90%, 95%, 98%, or99% identical to a fragment of the polypeptide, wherein the fragment isat least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% as long as thefull length wild type polypeptide or a domain thereof having an activityof interest, such as the ability to detect the presence of a definitiveendoderm cell or Pdx1-positive pancreatic progenitor. In someembodiments the domain is at least 100, 200, 300, or 400 amino acids inlength, beginning at any amino acid position in the sequence andextending toward the C-terminus. Variations known in the art toeliminate or substantially reduce the activity of the protein arepreferably avoided. In some embodiments, the variant lacks an N- and/orC-terminal portion of the full length polypeptide, e.g., up to 10, 20,or 50 amino acids from either terminus is lacking. In some embodimentsthe polypeptide has the sequence of a mature (full length) polypeptide,by which is meant a polypeptide that has had one or more portions suchas a signal peptide removed during normal intracellular proteolyticprocessing (e.g., during co-translational or post-translationalprocessing). In some embodiments wherein the protein is produced otherthan by purifying it from cells that naturally express it, the proteinis a chimeric polypeptide, by which is meant that it contains portionsfrom two or more different species. In some embodiments wherein aprotein is produced other than by purifying it from cells that naturallyexpress it, the protein is a derivative, by which is meant that theprotein comprises additional sequences not related to the protein solong as those sequences do not substantially reduce the biologicalactivity of the protein.

The term “functional fragments” as used herein is a polypeptide havingamino acid sequence which is smaller in size than, but substantiallyhomologous to the polypeptide it is a fragment of, and where thefunctional fragment polypeptide sequence is about at least 50%, or 60%or 70% or at 80% or 90% or 100% or greater than 100%, for example1.5-fold, 2-fold, 3-fold, 4-fold or greater than 4-fold effectivebiological action as the polypeptide from which it is a fragment of.Functional fragment polypeptides may have additional functions that caninclude decreased antigenicity, increased DNA binding (as intranscription factors), or altered RNA binding (as in regulating RNAstability or degradation).

The term “vector” refers to a carrier DNA molecule into which a DNAsequence can be inserted for introduction into a host cell. Preferredvectors are those capable of autonomous replication and/or expression ofnucleic acids to which they are linked Vectors capable of directing theexpression of genes to which they are operatively linked are referred toherein as “expression vectors”. Thus, an “expression vector” is aspecialized vector that contains the necessary regulatory regions neededfor expression of a gene of interest in a host cell. In some embodimentsthe gene of interest is operably linked to another sequence in thevector. Vectors can be viral vectors or non-viral vectors. Should viralvectors be used, it is preferred the viral vectors are replicationdefective, which can be achieved for example by removing all viralnucleic acids that encode for replication. A replication defective viralvector will still retain its infective properties and enters the cellsin a similar manner as a replicating adenoviral vector, however onceadmitted to the cell a replication defective viral vector does notreproduce or multiply. Vectors also encompass liposomes andnanoparticles and other means to deliver DNA molecule to a cell.

The term “operably linked” means that the regulatory sequences necessaryfor expression of the coding sequence are placed in the DNA molecule inthe appropriate positions relative to the coding sequence so as toeffect expression of the coding sequence. This same definition issometimes applied to the arrangement of coding sequences andtranscription control elements (e.g. promoters, enhancers, andtermination elements) in an expression vector. The term “operativelylinked” includes having an appropriate start signal (e.g., ATG) in frontof the polynucleotide sequence to be expressed, and maintaining thecorrect reading frame to permit expression of the polynucleotidesequence under the control of the expression control sequence, andproduction of the desired polypeptide encoded by the polynucleotidesequence.

The term “viral vectors” refers to the use of viruses, orvirus-associated vectors as carriers of a nucleic acid construct into acell. Constructs may be integrated and packaged into non-replicating,defective viral genomes like Adenovirus, Adeno-associated virus (AAV),or Herpes simplex virus (HSV) or others, including reteroviral andlentiviral vectors, for infection or transduction into cells. The vectormay or may not be incorporated into the cell's genome. The constructsmay include viral sequences for transfection, if desired. Alternatively,the construct may be incorporated into vectors capable of episomalreplication, e.g EPV and EBV vectors.

The terms “regulatory sequence” and “promoter” are used interchangeablyherein, and refer to nucleic acid sequences, such as initiation signals,enhancers, and promoters, which induce or control transcription ofprotein coding sequences with which they are operatively linked. In someexamples, transcription of a recombinant gene is under the control of apromoter sequence (or other transcriptional regulatory sequence) whichcontrols the expression of the recombinant gene in a cell-type in whichexpression is intended. It will also be understood that the recombinantgene can be under the control of transcriptional regulatory sequenceswhich are the same or which are different from those sequences whichcontrol transcription of the naturally-occurring form of a protein. Insome instances the promoter sequence is recognized by the syntheticmachinery of the cell, or introduced synthetic machinery, required forinitiating transcription of a specific gene.

As used herein, the term “transcription factor” refers to a protein thatbinds to specific parts of DNA using DNA binding domains and is part ofthe system that controls the transfer (or transcription) of geneticinformation from DNA to RNA. As used herein, “proliferating” and“proliferation” refer to an increase in the number of cells in apopulation (growth) by means of cell division. Cell proliferation isgenerally understood to result from the coordinated activation ofmultiple signal transduction pathways in response to the environment,including growth factors and other mitogens. Cell proliferation may alsobe promoted by release from the actions of intra- or extracellularsignals and mechanisms that block or negatively affect cellproliferation.

The term “selectable marker” refers to a gene, RNA, or protein that whenexpressed, confers upon cells a selectable phenotype, such as resistanceto a cytotoxic or cytostatic agent (e.g., antibiotic resistance),nutritional prototrophy, or expression of a particular protein that canbe used as a basis to distinguish cells that express the protein fromcells that do not. Proteins whose expression can be readily detectedsuch as a fluorescent or luminescent protein or an enzyme that acts on asubstrate to produce a colored, fluorescent, or luminescent substance(“detectable markers”) constitute a subset of selectable markers. Thepresence of a selectable marker linked to expression control elementsnative to a gene that is normally expressed selectively or exclusivelyin pluripotent cells makes it possible to identify and select somaticcells that have been reprogrammed to a pluripotent state. A variety ofselectable marker genes can be used, such as neomycin resistance gene(neo), puromycin resistance gene (puro), guanine phosphoribosyltransferase (gpt), dihydrofolate reductase (DHFR), adenosine deaminase(ada), puromycin-N-acetyltransferase (PAC), hygromycin resistance gene(hyg), multidrug resistance gene (mdr), thymidine kinase (TK),hypoxanthine-guanine phosphoribosyltransferase (HPRT), and hisD gene.Detectable markers include green fluorescent protein (GFP) blue,sapphire, yellow, red, orange, and cyan fluorescent proteins andvariants of any of these. Luminescent proteins such as luciferase (e.g.,firefly or Renilla luciferase) are also of use. As will be evident toone of skill in the art, the term “selectable marker” as used herein canrefer to a gene or to an expression product of the gene, e.g., anencoded protein.

In some embodiments the selectable marker confers a proliferation and/orsurvival advantage on cells that express it relative to cells that donot express it or that express it at significantly lower levels. Suchproliferation and/or survival advantage typically occurs when the cellsare maintained under certain conditions, i.e., “selective conditions”.To ensure an effective selection, a population of cells can bemaintained for a under conditions and for a sufficient period of timesuch that cells that do not express the marker do not proliferate and/ordo not survive and are eliminated from the population or their number isreduced to only a very small fraction of the population. The process ofselecting cells that express a marker that confers a proliferationand/or survival advantage by maintaining a population of cells underselective conditions so as to largely or completely eliminate cells thatdo not express the marker is referred to herein as “positive selection”,and the marker is said to be “useful for positive selection”. Negativeselection and markers useful for negative selection are also of interestin certain of the methods described herein. Expression of such markersconfers a proliferation and/or survival disadvantage on cells thatexpress the marker relative to cells that do not express the marker orexpress it at significantly lower levels (or, considered another way,cells that do not express the marker have a proliferation and/orsurvival advantage relative to cells that express the marker). Cellsthat express the marker can therefore be largely or completelyeliminated from a population of cells when maintained in selectiveconditions for a sufficient period of time.

A “reporter gene” as used herein encompasses any gene that isgenetically introduced into a cell that adds to the phenotype of thestem cell. Reporter genes as disclosed in this invention are intended toencompass fluorescent, luminescent, enzymatic and resistance genes, butalso other genes which can easily be detected by persons of ordinaryskill in the art. In some embodiments of the invention, reporter genesare used as markers for the identification of particular stem cells,cardiovascular stem cells and their differentiated progeny. A reportergene is generally operatively linked to sequences that regulate itsexpression in a manner dependent upon one or more conditions which aremonitored by measuring expression of the reporter gene. In some cases,expression of the reporter gene may be determined in live cells. Wherelive cell reporter gene assays are used, reporter gene expression may bemonitored at multiple timepoints, e.g., 2, 3, 4, 5, 6, 8, or 10 or moretimepoints. In some cases, where a live cell reporter assay is used,reporter gene expression is monitored with a frequency of at least about10 minutes to about 24 hours, e.g., 20 minutes, 1 hour, 2 hours, 3hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours,12 hours, 18 hours, or another frequency from any integer between about10 minutes to about 24 hours.

The terms “subject” and “individual” are used interchangeably herein,and refer to an animal, for example, a human from whom cells can beobtained and/or to whom treatment, including prophylactic treatment,with the cells as described herein, is provided. For treatment of thoseinfections, conditions or disease states which are specific for aspecific animal such as a human subject, the term subject refers to thatspecific animal. The “non-human animals” and “non-human mammals” as usedinterchangeably herein, includes mammals such as rats, mice, rabbits,sheep, cats, dogs, cows, pigs, and non-human primates. The term“subject” also encompasses any vertebrate including but not limited tomammals, reptiles, amphibians and fish. However, advantageously, thesubject is a mammal such as a human, or other mammals such as adomesticated mammal, e.g. dog, cat, horse, and the like, or productionmammal, e.g. cow, sheep, pig, and the like.

The terms “diabetes” and “diabetes mellitus” are used interchangeablyherein. The World Health Organization defines the diagnostic value offasting plasma glucose concentration to 7.0 mmol/l (126 mg/dl) and abovefor Diabetes Mellitus (whole blood 6.1 mmol/l or 110 mg/dl), or 2-hourglucose level 11.1 mmol/L or higher (200 mg/dL or higher). Other valuessuggestive of or indicating high risk for Diabetes Mellitus includeelevated arterial pressure 140/90 mm Hg or higher; elevated plasmatriglycerides (1.7 mmol/L; 150 mg/dL) and/or low HDL-cholesterol (lessthan 0.9 mmol/L, 35 mg/dl for men; less than 1.0 mmol/L, 39 mg/dLwomen); central obesity (males: waist to hip ratio higher than 0.90;females: waist to hip ratio higher than 0.85) and/or body mass indexexceeding 30 kg/m²; microalbuminuria, where the urinary albuminexcretion rate 20 μg/min or higher, or albumin:creatinine ratio 30 mg/gor higher). The term diabetes encompases all forms of diabetes, e.g.Type I, Type II and Type 1.5.

The terms “treat”, “treating”, “treatment”, etc., as applied to anisolated cell, include subjecting the cell to any kind of process orcondition or performing any kind of manipulation or procedure on thecell. As applied to a subject, the terms refer to providing medical orsurgical attention, care, or management to an individual. The individualis usually ill or injured, or at increased risk of becoming ill relativeto an average member of the population and in need of such attention,care, or management.

As used herein, the term “treating” and “treatment” refers toadministering to a subject an effective amount of a composition so thatthe subject as a reduction in at least one symptom of the disease or animprovement in the disease, for example, beneficial or desired clinicalresults. For purposes of this invention, beneficial or desired clinicalresults include, but are not limited to, alleviation of one or moresymptoms, diminishment of extent of disease, stabilized (i.e., notworsening) state of disease, delay or slowing of disease progression,amelioration or palliation of the disease state, and remission (whetherpartial or total), whether detectable or undetectable. Treating canrefer to prolonging survival as compared to expected survival if notreceiving treatment. Thus, one of skill in the art realizes that atreatment may improve the disease condition, but may not be a completecure for the disease. As used herein, the term “treatment” includesprophylaxis. Alternatively, treatment is “effective” if the progressionof a disease is reduced or halted. “Treatment” can also mean prolongingsurvival as compared to expected survival if not receiving treatment.Those in need of treatment include those already diagnosed with acardiac condition, as well as those likely to develop a cardiaccondition due to genetic susceptibility or other factors such as weight,diet and health.

As used herein, the terms “administering,” “introducing” and“transplanting” are used interchangeably in the context of the placementof cells, e.g. definitive endoderm cells or pdx1-positive pancreaticcells, or their differentiated progeny (e.g. insulin-producing cells orpancreatic β-cells or pancreatic β-like cells) of the invention into asubject, by a method or route which results in at least partiallocalization of the introduced cells at a desired site. The cells e.g.definitive endoderm cells or pdx1-positive pancreatic cells, or theirdifferentiated progeny (e.g. insulin-producing cells or pancreaticβ-cells or pancreatic β-like cells) an be implanted directly to thepancreas, or alternatively be administered by any appropriate routewhich results in delivery to a desired location in the subject where atleast a portion of the implanted cells or components of the cells remainviable. The period of viability of the cells after administration to asubject can be as short as a few hours, e.g. twenty-four hours, to a fewdays, to as long as several years. In some instances, the cells can alsobe administered at a non-pancreatic location, such as in the liver orsubcutaneously, for example, in a capsule to maintain the implantedcells at the implant location and avoid migration of the implantedcells.

The phrases “parenteral administration” and “administered parenterally”as used herein means modes of administration other than enteral andtopical administration, usually by injection, and includes, withoutlimitation, intravenous, intramuscular, intraarterial, intrathecal,intraventricular, intracapsular, intraorbital, intracardiac,intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular,intraarticular, sub capsular, subarachnoid, intraspinal, intracerebrospinal, and intrasternal injection and infusion. The phrases “systemicadministration,” “administered systemically”, “peripheraladministration” and “administered peripherally” as used herein mean theadministration of cardiovascular stem cells and/or their progeny and/orcompound and/or other material other than directly into the centralnervous system, such that it enters the animal's system and, thus, issubject to metabolism and other like processes, for example,subcutaneous administration.

The term “tissue” refers to a group or layer of specialized cells whichtogether perform certain special functions. The term “tissue-specific”refers to a source of cells from a specific tissue.

The term “halogen” refers to any radical of fluorine, chlorine, bromineor iodine.

The term “alkyl” refers to saturated non-aromatic hydrocarbon chainsthat may be a straight chain or branched chain, containing the indicatednumber of carbon atoms (these include without limitation propyl, allyl,or propargyl), which may be optionally inserted with N, O, S, S(O), orC(O). For example, C₁-C₆ indicates that the group may have from 1 to 6(inclusive) carbon atoms in it. Exemplary alkyl groups include, but arenot limited to, methyl, ethyl, propyl, isopropyl, butyl, t-butyl, andthe like.

The term “alkenyl” refers to an alkyl that comprises at least one doublebond. Exemplary alkenyl groups include, but are not limited to, forexample, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl and the like.

The term “alkynyl” refers to an alkyl that comprises at least one triplebond.

The term “alkylenyl” refers to a divalent group derived from a straightor branched chain alkyl. Exemplary alkylenyls include, but are notlimited to, —CH²—, —CH(CH₃)—, —C(CH₃)₂—, —CH₂CH₂—, —CH₂CH₂CH₂—,—CH₂CH₂CH₂CH₂—, —CH₂CH₂CH₂CH₂CH₂—, —CH₂CH₂CH₂CH₂CH₂CH₂—, and—CH₂CH(CH₃)CH₂—.

The term “alkenylenyl” refers to an alkylenyl that comprises at leastone double bond.

The term “alkynylenyl” refers to an alkylenyl that comprises at leastone triple bond.

The term “alkoxy” refers to an —O-alkyl radical.

The term “thioalkoxy” refers to an —S-alkyl radical.

The term “aryl” refers to monocyclic, bicyclic, or tricyclic aromaticring system wherein 0, 1, 2, 3, or 4 atoms of each ring may besubstituted by a substituent. Exemplary aryl groups include, but are notlimited to, phenyl, naphthyl, anthracenyl, azulenyl, fluorenyl, indanyl,indenyl, naphthyl, phenyl, tetrahydronaphthyl, and the like.

The term “cyclyl” refers to saturated and partially unsaturated cyclichydrocarbon groups having 3 to 12 carbons, for example, 3 to 8 carbons,and, for example, 3 to 6 carbons, wherein the cycloalkyl groupadditionally may be optionally substituted. Exemplary cycloalkyl groupsinclude, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl,cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, cyclooctyl, andthe like.

The term “heteroaryl” refers to an aromatic 5-8 membered monocyclic,8-12 membered bicyclic, or 11-14 membered tricyclic ring system having1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9heteroatoms if tricyclic, said heteroatoms selected from O, N, or S(e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S ifmonocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2, 3,or 4 atoms of each ring may be substituted by a substituent. Exemplaryheteroaryl groups include, but are not limited to, phenyl, pyridyl,furyl or furanyl, imidazolyl, benzimidazolyl, pyrimidinyl, thiophenyl orthienyl, pyridazinyl, pyrazinyl, quinolinyl, indolyl, thiazolyl,naphthyridinyl, and the like.

The term “heterocycyll” refers to a nonaromatic 5-8 membered monocyclic,8-12 membered bicyclic, or 11-14 membered tricyclic ring system having1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9heteroatoms if tricyclic, said heteroatoms selected from O, N, or S(e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S ifmonocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2 or 3atoms of each ring may be substituted by a substituent. Exemplaryheterocycyll groups include, but are not limited to piperazinyl,pyrrolidinyl, dioxanyl, morpholinyl, tetrahydrofuranyl, and the like.

The term “optionally substituted” means that the specified group ormoiety, such as an aryl group, heteroaryl group and the like, isunsubstituted or is substituted with one or more (typically 1-4substituents) independently selected from the group of substituentslisted below in the definition for “substituents” or otherwisespecified.

The term “substituents” refers to a group “substituted” on an alkyl,alkenyl, alkynyl, cycloalkyl, aryl, heterocycyll, or heteroaryl group atany atom of that group. Suitable substituents include, withoutlimitation, halo, hydroxy, oxo, nitro, haloalkyl, alkyl, alkenyl,alkynyl, alkaryl, aryl, aralkyl, alkoxy, aryloxy, amino, acylamino,alkylcarbanoyl, arylcarbanoyl, aminoalkyl, alkoxycarbonyl, carboxy,hydroxyalkyl, alkanesulfonyl, arenesulfonyl, alkanesulfonamido,arenesulfonamido, aralkylsulfonamido, alkylcarbonyl, acyloxy, cyano orureido. In some cases, two substituents, together with the carbons towhich they are attached to can form a ring.

The terms “decrease”, “reduced”, “reduction”, “decrease” or “inhibit”are all used herein generally to mean a decrease by a statisticallysignificant amount. However, for avoidance of doubt, “reduced”,“reduction” or “decrease” or “inhibit” means a decrease by at least 10%as compared to a reference level, for example a decrease by at leastabout 20%, or at least about 30%, or at least about 40%, or at leastabout 50%, or at least about 60%, or at least about 70%, or at leastabout 80%, or at least about 90% or up to and including a 100% decrease(i.e. absent level as compared to a reference sample), or any decreasebetween 10-100% as compared to a reference level.

The terms “increased”,“increase” or “enhance” or “activate” are all usedherein to generally mean an increase by a statically significant amount;for the avoidance of any doubt, the terms “increased”, “increase” or“enhance” or “activate” means an increase of at least 10% as compared toa reference level, for example an increase of at least about 20%, or atleast about 30%, or at least about 40%, or at least about 50%, or atleast about 60%, or at least about 70%, or at least about 80%, or atleast about 90% or up to and including a 100% increase or any increasebetween 10-100% as compared to a reference level, or at least about a2-fold, or at least about a 3-fold, or at least about a 4-fold, or atleast about a 5-fold or at least about a 10-fold increase, or anyincrease between 2-fold and 10-fold or greater as compared to areference level.

The term “statistically significant” or “significantly” refers tostatistical significance and generally means a two standard deviation(2SD) below normal, or lower, concentration of the marker. The termrefers to statistical evidence that there is a difference. It is definedas the probability of making a decision to reject the null hypothesiswhen the null hypothesis is actually true. The decision is often madeusing the p-value.

As used herein the term “comprising” or “comprises” is used in referenceto compositions, methods, and respective component(s) thereof, that areessential to the invention, yet open to the inclusion of unspecifiedelements, whether essential or not.

As used herein the term “consisting essentially of” refers to thoseelements required for a given embodiment. The term permits the presenceof additional elements that do not materially affect the basic and novelor functional characteristic(s) of that embodiment of the invention.

The term “consisting of” refers to compositions, methods, and respectivecomponents thereof as described herein, which are exclusive of anyelement not recited in that description of the embodiment.

As used in this specification and the appended claims, the singularforms “a,” “an,” and “the” include plural references unless the contextclearly dictates otherwise. Thus for example, references to “the method”includes one or more methods, and/or steps of the type described hereinand/or which will become apparent to those persons skilled in the artupon reading this disclosure and so forth.

It is understood that the foregoing detailed description and thefollowing examples are illustrative only and are not to be taken aslimitations upon the scope of the invention. Various changes andmodifications to the disclosed embodiments, which will be apparent tothose of skill in the art, may be made without departing from the spiritand scope of the present invention. Further, all patents, patentapplications, and publications identified are expressly incorporatedherein by reference for the purpose of describing and disclosing, forexample, the methodologies described in such publications that might beused in connection with the present invention. These publications areprovided solely for their disclosure prior to the filing date of thepresent application. Nothing in this regard should be construed as anadmission that the inventors are not entitled to antedate suchdisclosure by virtue of prior invention or for any other reason. Allstatements as to the date or representation as to the contents of thesedocuments are based on the information available to the applicants anddo not constitute any admission as to the correctness of the dates orcontents of these documents.

Stem Cells

Stem cells are cells that retain the ability to renew themselves throughmitotic cell division and can differentiate into a diverse range ofspecialized cell types. The two broad types of mammalian stem cells are:embryonic stem (ES) cells that are found in blastocysts, and adult stemcells that are found in adult tissues. In a developing embryo, stemcells can differentiate into all of the specialized embryonic tissues.In adult organisms, stem cells and progenitor cells act as a repairsystem for the body, replenishing specialized cells, but also maintainthe normal turnover of regenerative organs, such as blood, skin orintestinal tissues. Pluripotent stem cells can differentiate into cellsderived from any of the three germ layers.

While certain embodiments are described below in reference to the use ofstem cells for producing endoderm, e.g., definitive endoderm, germ cellsmay be used in place of, or with, the stem cells to provide endoderm,e.g., definitive endoderm, using similar protocols as the illustrativeprotocols described herein. Suitable germ cells can be prepared, forexample, from primordial germ cells present in human fetal materialtaken about 8-11 weeks after the last menstrual period. Illustrativegerm cell preparation methods are described, for example, in Shamblottet al., Proc. Natl. Acad. Sci. USA 95:13726, 1998 and U.S. Pat. No.6,090,622.

ES cells, e.g., human embryonic stem cells (hESCs) or mouse embryonicstem cells (mESCs), with a virtually endless replication capacity andthe potential to differentiate into most cell types, present, inprinciple, an unlimited starting material to generate the differentiatedcells for clinical therapy(http://stemcells.nih.gov/info/scireport/2006report.htm, 2006). Onepossible application of ES cells is to generate new pancreatic betacells for the cell replacement therapy of type I diabetics, by firstproducing endoderm, e.g., definitive endoderm, from, e.g., hESCs.

hESC cells, are described, for example, by Cowan et al. (N Engl. J. Med.350:1353, 2004) and Thomson et al. (Science 282:1145, 1998); embryonicstem cells from other primates, Rhesus stem cells (Thomson et al., Proc.Natl. Acad. Sci. USA 92:7844, 1995), marmoset stem cells (Thomson etal., Biol. Reprod. 55:254, 1996) and human embryonic germ (hEG) cells(Shamblott et al., Proc. Natl. Acad. Sci. USA 95:13726, 1998) may alsobe used in the methods disclosed herein. mESCs, are described, forexample, by Tremml et al. (Curr Protoc Stem Cell Biol. Chapter 1:Unit1C.4, 2008). The stem cells may be, for example, unipotent, totipotent,multipotent, or pluripotent. In some examples, any cells of primateorigin that are capable of producing progeny that are derivatives of atleast one germinal layer, or all three germinal layers, may be used inthe methods disclosed herein.

In certain examples, ES cells may be isolated, for example, as describedin Cowan et al. (N Engl. J. Med. 350:1353, 2004) and U.S. Pat. No.5,843,780 and Thomson et al., Proc. Natl. Acad. Sci. USA 92:7844, 1995.For example, hESCs cells can be prepared from human blastocyst cellsusing the techniques described by Thomson et al. (U.S. Pat. No.6,200,806; Science 282:1145, 1998; Curr. Top. Dev. Biol. 38:133 ff.,1998) and Reubinoff et al, Nature Biotech. 18:399, 2000. Equivalent celltypes to hESCs include their pluripotent derivatives, such as primitiveectoderm-like (EPL) cells, as outlined, for example, in WO 01/51610(Bresagen). hESCs can also be obtained from human pre-implantationembryos. Alternatively, in vitro fertilized (IVF) embryos can be used,or one-cell human embryos can be expanded to the blastocyst stage(Bongso et al., Hum Reprod 4: 706, 1989). Embryos are cultured to theblastocyst stage in G1.2 and G2.2 medium (Gardner et al., Fertil.Steril. 69:84, 1998). The zona pellucida is removed from developedblastocysts by brief exposure to pronase (Sigma). The inner cell massescan be isolated by immunosurgery, in which blastocysts are exposed to a1:50 dilution of rabbit anti-human spleen cell antiserum for 30 min,then washed for 5 min three times in DMEM, and exposed to a 1:5 dilutionof Guinea pig complement (Gibco) for 3 min (Solter et al., Proc. Natl.Acad. Sci. USA 72:5099, 1975). After two further washes in DMEM, lysedtrophectoderm cells are removed from the intact inner cell mass (ICM) bygentle pipetting, and the ICM plated on mEF feeder layers. After 9 to 15days, inner cell mass-derived outgrowths can be dissociated into clumps,either by exposure to calcium and magnesium-free phosphate-bufferedsaline (PBS) with 1 mM EDTA, by exposure to dispase or trypsin, or bymechanical dissociation with a micropipette; and then replated on mEF infresh medium. Growing colonies having undifferentiated morphology can beindividually selected by micropipette, mechanically dissociated intoclumps, and replated. ES-like morphology is characterized as compactcolonies with apparently high nucleus to cytoplasm ratio and prominentnucleoli. Resulting hESCs can then be routinely split every 1-2 weeks,for example, by brief trypsinization, exposure to Dulbecco's PBS(containing 2 mM EDTA), exposure to type IV collagenase (about 200 U/mL;Gibco) or by selection of individual colonies by micropipette. In someexamples, clump sizes of about 50 to 100 cells are optimal. mESCs cellscan be prepared from using the techniques described by e.g., Conner etal. (Curr. Prot. in Mol. Biol. Unit 23.4, 2003).

Embryonic stem cells can be isolated from blastocysts of members of theprimate species (U.S. Pat. No. 5,843,780; Thomson et al., Proc. Natl.Acad. Sci. USA 92:7844, 1995). Human embryonic stem (hES) cells can beprepared from human blastocyst cells using the techniques described byThomson et al. (U.S. Pat. No. 6,200,806; Science 282:1145, 1998; Curr.Top. Dev. Biol. 38:133 ff., 1998) and Reubinoff et al, Nature Biotech.18:399, 2000. Equivalent cell types to hES cells include theirpluripotent derivatives, such as primitive ectoderm-like (EPL) cells, asoutlined in WO 01/51610 (Bresagen).

Alternatively, in some embodiments, hES cells can be obtained from humanpreimplantation embryos. Alternatively, in vitro fertilized (IVF)embryos can be used, or one-cell human embryos can be expanded to theblastocyst stage (Bongso et al., Hum Reprod 4: 706, 1989). Embryos arecultured to the blastocyst stage in G1.2 and G2.2 medium (Gardner etal., Fertil. Steril. 69:84, 1998). The zona pellucida is removed fromdeveloped blastocysts by brief exposure to pronase (Sigma). The innercell masses are isolated by immunosurgery, in which blastocysts areexposed to a 1:50 dilution of rabbit anti-human spleen cell antiserumfor 30 min, then washed for 5 min three times in DMEM, and exposed to a1:5 dilution of Guinea pig complement (Gibco) for 3 min (Solter et al.,Proc. Natl. Acad. Sci. USA 72:5099, 1975). After two further washes inDMEM, lysed trophectoderm cells are removed from the intact inner cellmass (ICM) by gentle pipetting, and the ICM plated on mEF feeder layers.

After 9 to 15 days, inner cell mass-derived outgrowths are dissociatedinto clumps, either by exposure to calcium and magnesium-freephosphate-buffered saline (PBS) with 1 mM EDTA, by exposure to dispaseor trypsin, or by mechanical dissociation with a micropipette; and thenreplated on mEF in fresh medium. Growing colonies havingundifferentiated morphology are individually selected by micropipette,mechanically dissociated into clumps, and replated. ES-like morphologyis characterized as compact colonies with apparently high nucleus tocytoplasm ratio and prominent nucleoli. Resulting ES cells are thenroutinely split every 1-2 weeks by brief trypsinization, exposure toDulbecco's PBS (containing 2 mM EDTA), exposure to type IV collagenase(˜200 U/mL; Gibco) or by selection of individual colonies bymicropipette. Clump sizes of about 50 to 100 cells are optimal.

In some embodiments, human Embryonic Germ (hEG) cells are pluripotentstem cells which can be used in the methods as disclosed herein todifferentiate into primitive endoderm cells. hEG cells can be used beprepared from primordial germ cells present in human fetal materialtaken about 8-11 weeks after the last menstrual period. Suitablepreparation methods are described in Shamblott et al., Proc. Natl. Acad.Sci. USA 95:13726, 1998 and U.S. Pat. No. 6,090,622, which isincorporated herein in its entirety by reference.

Briefly, genital ridges processed to form disaggregated cells. EG growthmedium is DMEM, 4500 mg/L D-glucose, 2200 mg/L mM NaHCO₃; 15% ESqualified fetal calf serum (BRL); 2 mM glutamine (BRL); 1 mM sodiumpyruvate (BRL); 1000-2000 U/mL human recombinant leukemia inhibitoryfactor (LIF, Genzyme); 1-2 ng/mL human recombinant bFGF (Genzyme); and10 μM forskolin (in 10% DMSO). Ninety-six well tissue culture plates areprepared with a sub-confluent layer of feeder cells (e.g., STO cells,ATCC No. CRL 1503) cultured for 3 days in modified EG growth medium freeof LIF, bFGF or forskolin, inactivated with 5000 rad γ-irradiation ˜0.2mL of primary germ cell (PGC) suspension is added to each of the wells.The first passage is done after 7-10 days in EG growth medium,transferring each well to one well of a 24-well culture dish previouslyprepared with irradiated STO mouse fibroblasts. The cells are culturedwith daily replacement of medium until cell morphology consistent withEG cells is observed, typically after 7-30 days or 1-4 passages

In certain examples, the stem cells can be undifferentiated (e.g. a cellnot committed to a specific linage) prior to exposure to the compoundsof Formula (I) and subsequently Formula (II) according to the methods asdisclosed herein, whereas in other examples it may be desirable todifferentiate the stem cells to one or more intermediate cell typesprior to exposure of the compound(s) described herein. For example, thestems cells may display morphological, biological or physicalcharacteristics of undifferentiated cells that can be used todistinguish them from differentiated cells of embryo or adult origin. Insome examples, undifferentiated cells may appear in the two dimensionsof a microscopic view in colonies of cells with high nuclear/cytoplasmicratios and prominent nucleoli. The stem cells may be themselves (forexample, without substantially any undifferentiated cells being present)or may be used in the presence of differentiated cells. In certainexamples, the stem cells may be cultured in the presence of suitablenutrients and optionally other cells such that the stem cells can growand optionally differentiate. For example, embryonic fibroblasts orfibroblast-like cells may be present in the culture to assist in thegrowth of the stem cells. The fibroblast may be present during one stageof stem cell growth but not necessarily at all stages. For example, thefibroblast may be added to stem cell cultures in a first culturing stageand not added to the stem cell cultures in one or more subsequentculturing stages.

Stem cells used in all aspects of the present invention can be any cellsderived from any kind of tissue (for example embryonic tissue such asfetal or pre-fetal tissue, or adult tissue), which stem cells have thecharacteristic of being capable under appropriate conditions ofproducing progeny of different cell types, e.g. derivatives of all of atleast one of the 3 germinal layers (endoderm, mesoderm, and ectoderm).These cell types may be provided in the form of an established cellline, or they may be obtained directly from primary embryonic tissue andused immediately for differentiation. Included are cells listed in theNIH Human Embryonic Stem Cell Registry, e.g. hESBGN-01, hESBGN-02,hESBGN-03, hESBGN-04 (BresaGen, Inc.); HES-1, HES-2, HES-3, HES-4,HES-5, HES-6 (ES Cell International); Miz-hES1 (MizMedi Hospital-SeoulNational University); HSF-1, HSF-6 (University of California at SanFrancisco); and H1, H7, H9, H13, H14 (Wisconsin Alumni ResearchFoundation (WiCell Research Institute)). In some embodiments, the sourceof human stem cells or pluripotent stem cells used forchemically-induced differentiation into definitive endoderm cells didnot involve destroying a human embryo.

In another embodiment, the stem cells can be isolated from tissueincluding solid tissue. In some embodiments, the tissue is skin, fattissue (e.g. adipose tissue), muscle tissue, heart or cardiac tissue. Inother embodiments, the tissue is for example but not limited to,umbilical cord blood, placenta, bone marrow, or chondral

Stem cells of interest also include embryonic cells of various types,exemplified by human embryonic stem (hES) cells, described by Thomson etal. (1998) Science 282:1145; embryonic stem cells from other primates,such as Rhesus stem cells (Thomson et al. (1995) Proc. Natl. Acad. Sci.USA 92:7844); marmoset stem cells (Thomson et al. (1996) Biol. Reprod.55:254); and human embryonic germ (hEG) cells (Shambloft et al., Proc.Natl. Acad. Sci. USA 95:13726, 1998). Also of interest are lineagecommitted stem cells, such as mesodermal stem cells and other earlycardiogenic cells (see Reyes et al. (2001) Blood 98:2615-2625; Eisenberg& Bader (1996) Circ Res. 78(2):205-16; etc.) The stem cells may beobtained from any mammalian species, e.g. human, equine, bovine,porcine, canine, feline, rodent, e.g. mice, rats, hamster, primate, etc.In some embodiments, a human embryo was not destroyed for the source ofpluripotent cell used on the methods and compositions as disclosedherein.

ES cells are considered to be undifferentiated when they have notcommitted to a specific differentiation lineage. Such cells displaymorphological characteristics that distinguish them from differentiatedcells of embryo or adult origin. Undifferentiated ES cells are easilyrecognized by those skilled in the art, and typically appear in the twodimensions of a microscopic view in colonies of cells with highnuclear/cytoplasmic ratios and prominent nucleoli. Undifferentiated EScells express genes that may be used as markers to detect the presenceof undifferentiated cells, and whose polypeptide products may be used asmarkers for negative selection. For example, see U.S. application Ser.No. 2003/0224411 A1; Bhattacharya (2004) Blood 103(8):2956-64; andThomson (1998), supra., each herein incorporated by reference. Human EScell lines express cell surface markers that characterizeundifferentiated nonhuman primate ES and human EC cells, includingstage-specific embryonic antigen (SSEA)-3, SSEA-4, TRA-1-60, TRA-1-81,and alkaline phosphatase. The globo-series glycolipid GL7, which carriesthe SSEA-4 epitope, is formed by the addition of sialic acid to theglobo-series glycolipid GbS, which carries the SSEA-3 epitope. Thus, GL7reacts with antibodies to both SSEA-3 and SSEA-4. The undifferentiatedhuman ES cell lines did not stain for SSEA-1, but differentiated cellsstained strongly for SSEA-I. Methods for proliferating hES cells in theundifferentiated form are described in WO 99/20741, WO 01/51616, and WO03/020920.

A mixture of cells from a suitable source of endothelial, muscle, and/orneural stem cells can be harvested from a mammalian donor by methodsknown in the art. A suitable source is the hematopoieticmicroenvironment. For example, circulating peripheral blood, preferablymobilized (i.e., recruited) as described below, may be removed from asubject. Alternatively, bone marrow may be obtained from a mammal, suchas a human patient, undergoing an autologous transplant. In someembodiments, stem cells can be obtained from the subjects adiposetissue, for example using the CELUTION™ SYSTEM from Cytori, as disclosedin U.S. Pat. Nos. 7,390,484 and 7,429,488 which is incorporated hereinin its entirety by reference.

In some embodiments, human umbilical cord blood cells (HUCBC) are usefulin the methods as disclosed herein. Human UBC cells are recognized as arich source of hematopoietic and mesenchymal progenitor cells (Broxmeyeret al., 1992 Proc. Natl. Acad. Sci. USA 89:4109-4113). Previously,umbilical cord and placental blood were considered a waste productnormally discarded at the birth of an infant. Cord blood cells are usedas a source of transplantable stem and progenitor cells and as a sourceof marrow repopulating cells for the treatment of malignant diseases(i.e. acute lymphoid leukemia, acute myeloid leukemia, chronic myeloidleukemia, myelodysplastic syndrome, and nueroblastoma) and non-malignantdiseases such as Fanconi's anemia and aplastic anemia (Kohli-Kumar etal., 1993 Br. J. Haematol. 85:419-422; Wagner et al., 1992 Blood 79;1874-1881; Lu et al., 1996 Crit. Rev. Oncol. Hematol 22:61-78; Lu etal., 1995 Cell Transplantation 4:493-503). A distinct advantage of HUCBCis the immature immunity of these cells that is very similar to fetalcells, which significantly reduces the risk for rejection by the host(Taylor & Bryson, 1985J. Immunol. 134:1493-1497). Human umbilical cordblood contains mesenchymal and hematopoietic progenitor cells, andendothelial cell precursors that can be expanded in tissue culture(Broxmeyer et al., 1992 Proc. Natl. Acad. Sci. USA 89:4109-4113;Kohli-Kumar et al., 1993 Br. J. Haematol. 85:419-422; Wagner et al.,1992 Blood 79; 1874-1881; Lu et al., 1996 Crit. Rev. Oncol. Hematol22:61-78; Lu et al., 1995 Cell Transplantation 4:493-503; Taylor &Bryson, 1985J. Immunol. 134:1493-1497 Broxmeyer, 1995 Transfusion35:694-702; Chen et al., 2001 Stroke 32:2682-2688; Nieda et al., 1997Br. J. Haematology 98:775-777; Erices et al., 2000 Br. J. Haematology109:235-242). The total content of hematopoietic progenitor cells inumbilical cord blood equals or exceeds bone marrow, and in addition, thehighly proliferative hematopoietic cells are eightfold higher in HUCBCthan in bone marrow and express hematopoietic markers such as CD14,CD34, and CD45 (Sanchez-Ramos et al., 2001 Exp. Neur. 171:109-115;Bicknese et al., 2002 Cell Transplantation 11:261-264; Lu et al., 1993J. Exp Med. 178:2089-2096).

In another embodiment, pluripotent cells are cells in the hematopoieticmicro-environment, such as the circulating peripheral blood, preferablyfrom the mononuclear fraction of peripheral blood, umbilical cord blood,bone marrow, fetal liver, or yolk sac of a mammal. The stem cells,especially neural stem cells, may also be derived from the centralnervous system, including the meninges.

In another embodiment, pluripotent cells are present in embryoid bodiesare formed by harvesting ES cells with brief protease digestion, andallowing small clumps of undifferentiated human ESCs to grow insuspension culture. Differentiation is induced by withdrawal ofconditioned medium. The resulting embryoid bodies are plated ontosemi-solid substrates. Formation of differentiated cells may be observedafter around about 7 days to around about 4 weeks. Viabledifferentiating cells from in vitro cultures of stem cells are selectedfor by partially dissociating embryoid bodies or similar structures toprovide cell aggregates. Aggregates comprising cells of interest areselected for phenotypic features using methods that substantiallymaintain the cell to cell contacts in the aggregate.

In an alternative embodiment, the stem cells can be reprogrammed stemcells, such as stem cells derived from somatic or differentiated cells.In such an embodiment, the de-differentiated stem cells can be forexample, but not limited to, neoplastic cells, tumor cells and cancercells or alternatively induced reprogrammed cells such as inducedpluripotent stem cells or iPS cells.

Cloning and Cell Culture

Illustrative methods for molecular genetics and genetic engineering thatmay be used in the technology described herein may be found, forexample, in current editions of Molecular Cloning: A Laboratory Manual,(Sambrook et al., Cold Spring Harbor); Gene Transfer Vectors forMammalian Cells (Miller & Calos eds.); and Current Protocols inMolecular Biology (F. M. Ausubel et al. eds., Wiley & Sons). Cellbiology, protein chemistry, and antibody techniques can be found, forexample, in Current Protocols in Protein Science (J. E. Colligan et al.eds., Wiley & Sons); Current Protocols in Cell Biology (J. S. Bonifacinoet al., Wiley & Sons) and Current protocols in Immunology (J. E.Colligan et al. eds., Wiley & Sons.). Illustrative reagents, cloningvectors, and kits for genetic manipulation may be commercially obtained,for example, from BioRad, Stratagene, Invitrogen, ClonTech, andSigma-Aldrich Co.

Suitable cell culture methods may be found, for example, in Cell culturemethods are described generally in the current edition of Culture ofAnimal Cells: A Manual of Basic Technique (R. I. Freshney ed., Wiley &Sons); General Techniques of Cell Culture (M. A. Harrison & I. F. Rae,Cambridge Univ. Press), and Embryonic Stem Cells: Methods and Protocols(K. Turksen ed., Humana Press). Suitable tissue culture supplies andreagents are commercially available, for example, from Gibco/BRL,Nalgene-Nunc International, Sigma Chemical Co., and ICN Biomedicals.

Pluripotent stem cells can be propagated by one of ordinary skill in theart and continuously in culture, using culture conditions that promoteproliferation without promoting differentiation. Exemplaryserum-containing ES medium is made with 80% DMEM (such as Knock-OutDMEM, Gibco), 20% of either defined fetal bovine serum (FBS, Hyclone) orserum replacement (WO 98/30679), 1% non-essential amino acids, 1 mML-glutamine, and 0.1 mM .beta.-mercaptoethanol. Just before use, humanbFGF is added to 4 ng/mL (WO 99/20741, Geron Corp.). Traditionally, EScells are cultured on a layer of feeder cells, typically fibroblastsderived from embryonic or fetal tissue.

Scientists at Geron have discovered that pluripotent SCs can bemaintained in an undifferentiated state even without feeder cells. Theenvironment for feeder-free cultures includes a suitable culturesubstrate, particularly an extracellular matrix such as Matrigel® orlaminin. Typically, enzymatic digestion is halted before cells becomecompletely dispersed (say, .about.5 min with collagenase IV). Clumps of˜10 to 2,000 cells are then plated directly onto the substrate withoutfurther dispersal.

Feeder-free cultures are supported by a nutrient medium containingfactors that support proliferation of the cells without differentiation.Such factors may be introduced into the medium by culturing the mediumwith cells secreting such factors, such as irradiated (˜4,000 rad)primary mouse embryonic fibroblasts, telomerized mouse fibroblasts, orfibroblast-like cells derived from pPS cells. Medium can be conditionedby plating the feeders at a density of ˜5-6×10⁴ cm⁻² in a serum freemedium such as KO DMEM supplemented with 20% serum replacement and 4ng/mL bFGF. Medium that has been conditioned for 1-2 days issupplemented with further bFGF, and used to support pluripotent SCculture for 1-2 days. Features of the feeder-free culture method arefurther discussed in International Patent Publication WO 01/51616; andXu et al., Nat. Biotechnol. 19:971, 2001.

Under the microscope, ES cells appear with high nuclear/cytoplasmicratios, prominent nucleoli, and compact colony formation with poorlydiscernable cell junctions. Primate ES cells express stage-specificembryonic antigens (SSEA) 3 and 4, and markers detectable usingantibodies designated Tra-1-60 and Tra-1-81 (Thomson et al., Science282:1145, 1998). Mouse ES cells can be used as a positive control forSSEA-1, and as a negative control for SSEA-4, Tra-1-60, and Tra-1-81.SSEA-4 is consistently present human embryonal carcinoma (hEC) cells.Differentiation of pluripotent SCs in vitro results in the loss ofSSEA-4, Tra-1-60, and Tra-1-81 expression, and increased expression ofSSEA-1, which is also found on undifferentiated hEG cells.

In accordance with certain examples, several approaches may combinedwith methods of the invention to differentiate the stem cells toendoderm cells. In one approach, the stem cells may be plated onto a newsubstrate or the medium may be exchanged to remove extracellular matrixor soluble factors that inhibit differentiation. This is sometimesreferred to as the “direct differentiation method”, and is described ingeneral terms in International patent publication WO 01/51616, and U.S.Patent Publication 2002/0019046, which is incorporated herein in itsentirety by reference. It is usually preferable in the directdifferentiation method to begin with a feeder-free culture of stemcells, so as to avoid potential complications in the differentiationprocess caused by residual feeder cells. Another approach is to putundifferentiated stem cells in suspension culture, which will frequentlycause them to form aggregates of differentiated and undifferentiatedcells. For example, stem cells can be harvested by brief collagenasedigestion, dissociated into clusters, and passaged in non-adherent cellculture plates. The aggregates can be fed every few days, and thenharvested after a suitable period, typically 4-8 days. Depending on theconditions, aggregates generally start by forming a heterogeneouspopulation of cell types, including a substantial frequency of endodermcells. The aggregates can then be dispersed and replated for the nextstage in the differentiation process, on substrates such as laminin orfibronectin; or passaged in suspension culture using, for example,non-adherent plates and a suitable medium. In some instances,differentiation can take place in the presence of one or more of thecompounds of Formula (I) or Formula (II) as described herein, e.g., IDE1and/or IDE2.

Direct differentiation or differentiation in aggregates can be monitoredfor the presence of endoderm cells using suitable markers such as thoselisted in U.S. Pat. No. 7,326,572. In some preferred embodiments,differentiation can be monitored for the presence of endoderm cellsusing markers such as Sox17. Once a sufficient proportion of endoderm isobtained, cells can be replated or otherwise manipulated to beginanother stage of differentiation. In certain circumstances,differentiation or maintenance of cells may be enhanced if the cells arekept in micromass clusters (for example, 50 to 5,000 cells).

Compounds for Inducing the Differentiation of Pluripotent Stem Cells toDefinitive Endoderm Cells

One aspect of the present invention provides methods of producing anendoderm cell, e.g. a definitive endoderm cell by contacting (e.g.,culturing) a pluripotent stem cell with a compound of Formula (I) asdescribed herein. Accordingly, in some embodiments any compound withFormula (I) useful in the methods and compositions as disclosed hereinare cell permeable small molecules, and can control cellular processesby modulating signal transduction pathways, gene expression ormetabolism and have been effectively used in stem cell differentiationprotocols. Small molecules can be synthesized in high quantity andpurity as well as conveniently supplied or removed, giving them greatpotential to be useful for therapeutic applications. High throughputscreens have been performed to identify novel small molecules that cansupport the self renewal of ES cells (Chen et al., 2006; Desbordes etal., 2008), cardiogenic specification of mouse ES cells (Wu et al.,2004) or neural progenitor cells (Diamandis et al., 2007) as well asinducing specific cell types, notably neuronal and muscle cells(reviewed by (Ding and Schultz, 2004).

In one embodiment, a pluripotent stem cell, such as a human pluripotentstem cell is contacted with at least one compound of Formula (I) todifferentiate the pluripotent stem cell into endoderm, such asdefinitive endoderm.

In one aspect, the invention provides a method of producing a definitiveendoderm cell from a pluripotent stem cell comprising contacting apopulation of pluripotent stem cells with at least one compound ofFormula (I) to induce the differentiation of at least one pluripotentstem cell into a definitive endoderm cell, wherein the definitiveendoderm cell expresses Sox17, or HNF3B (FoxA2), or Sox17 and HNF3B(FoxA2) and wherein the compound of formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

In some embodiments, R¹ is H or C₁-C₆ alkyl. Preferred alkyls for R¹include methyl, ethyl, propyl, isopropyl or t-butyl. Preferably R¹ is H.

In some embodiments, R² is H or C₁-C₆ alkyl. Preferred alkyls for R²include methyl, ethyl, propyl, isopropyl or t-butyl.

In some embodiments, R³ is H or an optionally substituted aryl orheteroaryl. A preferred aryl for R³ is an optionally substituted phenyl.Preferably R³ is a phenyl substituted with —C(O)OR⁵, where R⁵ is H,alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or cyclyl, each ofwhich can be optionally substituted. Preferably, R⁵ is H, methyl, ethyl,or t-butyl.

In one embodioment, R³ is

In some embodiments, R⁴ is H or C₁-C₆ alkyl. Preferred alkyls for R⁴include methyl, ethyl or propyl.

In some embodiments, R³ and R⁴ together with the carbon to which theyare attached form an optionally substituted cyclyl or heterocycyll. Inone embodiment, R³ and R⁴ together with the carbon to which they areattached form a 5-8 membered cyclyl. Preferably cyclyl is a 5 membered.

In some embodiments, L is a C₁-C₁₀ alkylenyl. Preferably L is—CH₂CH₂CH₂CH₂CH₂—.

In a preferred compound of formula (I), R¹, R², and R⁴ are H and R³ isan optionally substituted aryl or heteroaryl.

In another preferred compound of formula (I), R¹ and R² are H and R³ andR⁴ together with the carbon they are attached to form an optionallysubstituted 5-8 membered cyclyl of heterocylyl.

One preferred compound of formula (I) is IDE1, wherein IDE1 has thefollowing structure:

Another preferred compound of formula (I) is IDE2, wherein IDE2 has thefollowing structure:

In alternative embodiments, a pluripotent stem cell, such as a humanpluripotent stem cell is contacted with at least one histone deacetylase(HDAC) inhibitor (e.g., a class I/II HDAC inhibitor) to differentiatethe pluripotent stem cell into endoderm, such as definitive endoderm.Histone deacetylase (HDAC) are a class of enzymes that remove acetylgroups from an ε-N-acetyl lysine amino acid on a histone. ExemplaryHDACs include those Class I HDAC: HDAC1, HDAC2, HDAC3, HDAC8; and ClassII HDACs: HDAC4, HDACS, HDAC6, HDAC7A, HDAC9, HDAC10. Type I mammalianHDACs include: HDAC1, HDAC2, HDAC3, HDAC8, and HDAC11. Type II mammalianHDACs include: HDAC4, HDACS, HDAC6, HDAC7, HDAC9, and HDAC1.

A number of structural classes of negative regulators of HDACs (e.g.,HDAC inhibitors) have been developed, for example, small molecularweight carboxylates (e.g., less than about 250 amu), hydroxamic acids,benzamides, epoxyketones, cyclic peptides, and hybrid molecules. (See,for example, Drummond D C, Noble C O, Kirpotin D B, Guo Z, Scott G K, etal. (2005) Clinical development of histone deacetylase inhibitors asanticancer agents. Annu Rev Pharmacol Toxicol 45: 495-528, (includingspecific examples therein) which is hereby incorporated by reference inits entirety). Non-limiting examples of negative regulators of type I/IIHDACs include: Suberoylanilide Hydroxamic Acid (SAHA (e.g., MK0683,vorinostat) and other hydroxamic acids), BML-210, Depudecin (e.g.,(−)-Depudecin), HC Toxin, Nullscript(4-(1,3-Dioxo-1H,3H-benzo[de]isoquinolin-2-yl)-N-hydroxybutanamide),Phenylbutyrate (e.g., sodium phenylbutyrate) and Valproic Acid ((VPA)and other short chain fatty acids), Scriptaid, Suramin Sodium,Trichostatin A (TSA), APHA Compound 8, Apicidin, Sodium Butyrate,pivaloyloxymethyl butyrate (Pivanex, AN-9), Trapoxin B, Chlamydocin,Depsipeptide (also known as FR901228 or FK228), benzamides (e.g., CI-994(i.e., N-acetyl dinaline) and MS-27-275), MGCD0103, NVP-LAQ-824, CBHA(m-carboxycinnaminic acid bishydroxamic acid), JNJ16241199, Tubacin,A-161906, proxamide, oxamflatin, 3-Cl-UCHA (i.e.,6-(3-chlorophenylureido)caproic hydroxamic acid), AOE(2-amino-8-oxo-9,10-epoxydecanoic acid), CHAP31, CHAP 50, IDE1 and IDE2.Other inhibitors include, for example, dominant negative forms of theHDACs (e.g., catalytically inactive forms) siRNA inhibitors of theHDACs, and antibodies that specifically bind to the HDACs. Inhibitorsare available, e.g., from BIOMOL International, Fukasawa, MerckBiosciences, Novartis, Gloucester Pharmaceuticals, Aton Pharma, TitanPharmaceuticals, Schering AG, Pharmion, MethylGene, and Sigma Aldrich.In some embodiments, IDE1 or IDE2 is a preferred histone deacetylaseinhibitor.

In some embodiments of this aspect of the present invention providesmethods of producing a definitive endoderm cell by contacting (e.g.,culturing) a pluripotent stem cell, e.g. an iPS cell or embryonic stemcell with a compound of Formula (I) as described herein, wherein the apluripotent stem cell is contacted with a compound of Formula (I) at aconcentration of about between 25 nM to 10 μM, or between about 25 nM to50 nM, or about 50 nM to 100 nM, or about 100 nM to 200 nM, or about 200nM to about 500 nM or about 500 nM to about 1 μM, or about 1 μM to 2 μm,or about 2 μM to 5 μm, or about 5 μM to 10 μM.

In some embodiments, methods of producing a definitive endoderm cell bycontacting (e.g., culturing) a pluripotent stem cell, e.g. an iPS cellor embryonic stem cell with a compound of Formula (I) at a concentrationof at least about 5 nM, at least about 7 nM, at least about 10 nM, atleast about 12 nM, at least about 15 nM, at least about 17 nM, at leastabout 20 nM, at least about 25 nM, at least about 30 nM, at least about35 nM, at least about 40 nM, at least about 45 nM, at least about 50 nM,at least about 100 nM or at least about 200 nM, or at least about 300 nMor at least about 400 nM or at least about 500 nM or more than 500 nM,or any inter between 10-500 nM or any inter between 5-50 nM, or anyinteger between 50-100 nM, or any integer between 100 nM-200 nM or anyinteger between 200 nM-500 nM. In some embodiments, a pluripotent stemcell is contacted (e.g. cultured) with a compound of Formula (I) at aconcentration of at least about 0.1 μM, or at least about 0.2 μM, or atleast about 0.3 μM, or at least about 0.4 μM, or at least about 0.5 μM,or at least about 1 μM, at least about 1.5 μM, at least about 2 μM, atleast about 2.5 μM, at least about 3 μM, at least about 3.5 μM, at leastabout 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 6μM, at least about 7 μM, at least about 8 μM, at least about 9 μM, or atleast about 10 μM, or more than 10 μM, or any inter between 0.1-0.5 μMor any integer between about 0.5-10 μM or any inter between 0.1-10 μM,or any integer between 0.5-5 μM, or any integer between 5 μM-10 μM.

In some embodiments, a pluripotent stem cell is contacted (e.g.cultured) with a compound of Formula (I) which is IDE1, such that thepluripotent stem cell is differentiated into a definitive endoderm cellby contacting (e.g. culturing) the pluripotent stem cell with IDE1 at aconcentration of at least about at least about 20 nM, or at least about25 nM, at least about 30 nM, at least about 35 nM, at least about 40 nM,at least about 45 nM, at least about 50 nM, or at least about 60 nM, orat least about 70 nM, or at least about 80 nM, or at least about 90 nM,or at least about 100 nM or at least about 200 nM, or at least about 300nM or at least about 400 nM or at least about 500 nM or more than 500nM, or any inter between 20-500 nM or any inter between 50-100 nM, orany integer between 50-150 nM, or any integer between 100 nM-200 nM orany integer between 200 nM-500 nM. In some embodiments, the pluripotentstem cell is contacted with a compound of IDE1 at a concentration ofabout 100 nM to differentiate the pluripotent stem cell into adefinitive endoderm cell.

In some embodiments, a pluripotent stem cell is contacted (e.g.cultured) with a compound of Formula (I) which is IDE2, such that thepluripotent stem cell is differentiated into a definitive endoderm cellby contacting (e.g. culturing) the pluripotent stem cell with IDE2 at aconcentration of at least about at least about 20 nM, or at least about25 nM, at least about 30 nM, at least about 35 nM, at least about 40 nM,at least about 45 nM, at least about 50 nM, or at least about 60 nM, orat least about 70 nM, or at least about 80 nM, or at least about 90 nM,or at least about 100 nM or at least about 200 nM, or at least about 300nM or at least about 400 nM or at least about 500 nM or more than 500nM, or any inter between 20-500 nM or any inter between 50-200 nM, orany integer between 100-300 nM, or any integer between 100 nM-500 nM orany integer between about 200 nM-500 nM. In some embodiments, thepluripotent stem cell is contacted with a compound of IDE2 at aconcentration of about 200 nM to differentiate the pluripotent stem cellinto a definitive endoderm cell.

In some embodiments, a population of pluripotent stem cells can becontacted or exposed to one or more of the compounds of Formula (I),e.g. IDE1 or IDE2 as described herein alone, and in other embodiments, apopulation of pluripotent stem cells can be contacted with at least oneadditional agent, either concurrent with (e.g. in combination with),subsequent to or prior to the contact of the pluripotent cell with acompound of Formula (I). In some embodiments, the additional compoundfor use in combination with compounds of Formula (I) can include, but isnot limited to agents of transforming growth factor-13 (TGF-β) familymember (e.g., Nodal or Activin A), fibroblast growth factor (FGF) familymember (e.g., FGF10), Wnt growth factor family member (e.g., Wnt3a),bone morphogenic proteins (BMPs) and/or members of the AKT/PI3K pathway.The definition and details of the TGF-β/BMP pathway are disclosed in theart e.g., Kawabata M. and Miyazono K., J. Biochem. (Tokyo), 125, 9-16(1999); Wrana J. L., Miner. Electrolyte Metab., 24, 120-130 (1998); andMarkowitz S. D., and Roberts A. B., Cytokine Growth Factor Rev., 7,93-102 (1996). In some embodiments, a pluripotent stem cell can beexposed to a compound of Formula (I), e.g. IDE1 and/or IDE2 incombination with at least one additional compounds or factors including,but not limited to cyclopamine, TGF family members (TGF-alpha., ActivinA, Activin B, TGF-beta-1, TGF-beta-3), exendin 4, nicotinamide,n-butyrate, DMSO, all-trans retinoic acid, GLP-I, bone morphogenicproteins (BMP-2, BMP-5, BMP-6, BMP-7), insulin-like growth factors(IGF-I, IGF-II), fibroblast growth factor (FGF7, FGF10, bFGF, FGF4),other growth factors (EGF, βcellulin, growth hormone, HGF), otherhormones (prolactin, cholecytokinin, gastrin I, placental lactogen),TGF-β. family antagonists (Noggin, follistatin, chordin), IBMX,wortmannin, dexamethazone, Reg, INGAP, cAMP or cAMP activators(forskolin), and/or extracellular matrix components (laminin,fibronectin).

Endoderm Cells and Definitive Endoderm Cells

In certain examples, the agents such as compounds of Formula (I) can beused to induce the differentiation of pluripotent stem cells intoendoderm cells, e.g., definitive endoderm cells by exposing orcontacting a population of pluripotent stem cells with an effectiveamount of at least one compound of Formula (I) as described herein todifferentiate the stem cells into an endoderm cell, e.g., a definitiveendoderm cell. Accordingly, included herein are cells and compositionsmade by the methods described herein. The exact amount and type ofcompound of Formula (I) can vary depending on the number of pluripotentstem cells, the desired differentiation stage and the number of priordifferentiation stages that have been performed.

In certain examples, a compound of Formula (I) is present in aneffective amount. As used herein, “effective amount” refers to theamount of the compound that should be present for the differentiation ofat least 10% or at least 20% or at least 30% of the cells in apopulation of pluripotent stem cell, e.g. an ES cells or iPS cells intoendoderm cells, such as definitive endoderm cells. In additionalexamples, a compound of Formula (I) such as IDE1 or IDE2 can be presentin the culture medium of the pluripotent stem cells e.g. the ES cells,or alternatively, the compounds of Formula (I) such as IDE1 or IDE2 maybe added to the ES cells during some stage of growth. In some examples,a compound of Formula (I), e.g., IDE1 and/or IDE2 is used to produce thepancreatic cells or pancreatic cell precursors, and the HDACinhibitor(s), e.g., IDE1 and/or IDE2 can be present in a concentrationof about 10 μM/liter or less, for example about 1 μM/liter or less. Incertain examples, a population of pluripotent stem cells can be exposedto at least one compound of Formula (I), e.g. IDE1 and/or IDE2 prior toany differentiation or during the first stage of differentiation.

Endoderm is one of the germ layers formed during animal embryogenesis.Cells generally migrate inward along the archenteron from the innerlayer of the gastrula, which develops into the endoderm. Exemplaryproducts produced by the endoderm include: gastrointestinal tract,respiratory tract, endocrine glands and organs (e.g., liver andpancreas). The endoderm generally consists at first of flattened cells,which subsequently become columnar. It can form the epithelial lining ofthe whole of the digestive tube except part of the mouth, pharynx andthe terminal part of the rectum (which are lined by involutions of theectoderm), the lining cells of all the glands which open into thedigestive tube, including those of the liver and pancreas, theepithelium of the auditory tube and tympanic cavity, of the trachea,bronchi, and alveoli of the lungs, of the urinary bladder and part ofthe urethra, and that which lines the follicles of the thyroid gland andthymus.

Exemplary studies of the developmental pathways that control endodermformation have been conducted in Xenopous laevis, zebrafish and mice(reviewed by Wells and Melton, 1999; Lewis and Tam, 2006). Collectively,these studies suggest a conserved mechanism for endoderm/mesodermcommitment utilizing the transforming growth factor-β (TGF-β) familymember Activin A and Nodal, fibroblast growth factor (FGF) and Wntgrowth factor families. Similarly, in vitro application of Activin A orNodal to mouse or human ES cell cultures leads to endoderm induction(Kubo et al., 2004; Yasunaga et al., 2005; D'Amour et al., 2005). Othermolecules that influence endoderm formation in vitro include WNTs(D'Amour et al., 2005), bone morphogenic proteins (BMPs), and members ofthe AKT/PI3K pathway (McLean et al., 2007).

In certain examples, a method of inducing the differentiation ofpluripotent stem cells, e.g. embryonic stem cells to endoderm cells,e.g., definitive endoderm cells, is provided. In some examples, themethod comprises providing a pluripotent stem cell, e.g. an embryonicstem cell and providing at least one compound of Formula (I) asdescribed herein to differentiate the pluripotent stem cell, e.g. anembryonic stem cell, to provide the endoderm cell, e.g. a definitiveendoderm cell, upon exposure of the pluripotent stem cell to thecompound. In certain examples, the compound may be present in aneffective amount in the culture medium or may be added to the culturemedium at a desired stage. In some examples, the compound may be IDE1and/or IDE2. In certain examples, a population of pluripotent stem cellsmay be exposed to a compound of Formula (I) prior to any differentiationor during the first stage of differentiation.

In certain embodiments, a method of producing an endoderm cell, e.g., adefinitive endoderm cell from a pluripotent stem cells, e.g. anembryonic stem cells is disclosed. In one example, the method comprisesculturing the pluripotent stem cell, e.g. an embryonic stem cells in aculture medium comprising an effective amount of at least one compoundof Formula (I) as described herein, e.g. IDE1 and/or IDE2, to induce andcause the differentiation of at least one pluripotent stem cell into anendoderm cell, e.g., a definitive endoderm cell. In certain examples,the compound of Formula (I) is IDE1 and/or IDE2. In some embodiments, apopulation of pluripotent stem cells are cultured in the presence of thecompound of Formula (I) prior to any differentiation or during the firststage of differentiation.

In certain examples, a method of producing endoderm, e.g., definitiveendoderm, by culturing stem cells in the presence of an effective amountof at least one compound of Formula (I), such as IDE1 or IDE2 describedherein is provided to thereby produce an endoderm cell, e.g., andefinitive endoderm cell is provided. One can use any pluripotent stemcell, such as a human pluripotent stem cell, or a human iPS cell or anyof pluripotent stem cell as discussed herein or other suitablepluripotent stem cells. In some embodiments, a compound of Formula (I)as described herein can be present in the culture medium of a populationof pluripotent stem cells or may be added in bolus or periodicallyduring growth (e.g. replication or propagation) of the population ofpluripotent stem cells. In certain examples, a population of pluripotentstem cells can be exposed to at least one compound of Formula (I) priorto any differentiation. In other examples, a population of pluripotentstem cells may be exposed to at least one compound of Formula (I) e.g.IDE1 or IDE2 during the first stage of differentiation.

Confirmation of the Presence and the Identification of a DefinitiveEndoderm Cell

One can use any means common to one of ordinary skill in the art toconfirm the presence of an endoderm cell, e.g. a definitive endodermcell produced the induction of the differentiation of a pluripotent stemcell by exposure to a compound of Formula (I), such as IDE1 and/or IDE2.In some embodiments, the presence of endoderm cells can be detectedusing suitable markers such as those listed in U.S. Pat. No. 7,326,572,which is incorporated herein by reference.

In some embodiments, the presence of definitive endoderm markers, e.g.chemically induced definitive endoderm cells, can be done by detectingthe presence or absence of one or more markers indicative of andefinitive endoderm cell. In some embodiments, the method can includedetecting the positive expression (e.g. the presence) of a marker fordefinitive endoderm cells. In some embodiments, the marker can bedetected using a reagent, e.g., a reagent for the detection of SOX17,HNF3β (Fox2A), MIXL2, GATA4, GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1,CRIP1. In particular, definitive endoderm cells herein express Sox17and/or HNF3B, and do not express significant levels of extra-embryonicendoderm markers GATA4, SPARC, APF or DAB. Other positive markers fordefinitive endoderm cells also include, for example as shown in FIG. 4A,Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4, Rab15, Npnt,Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1 and Rbm35a. Negativemarkers (e.g. the absence of significant levels of expression) fordefinitive endoderm cells include extra-embryonic (EE) endoderm markerssuch as Gata4, SPARC, APF and DAB, as well as negative markers Zic,Pax6, Flk1 or CD31. Negative markers of definitive endoderm cells areuseful for the purposes of negative selection of non-definitive endodermcells (e.g. selection and discarding cells which express Gata4, SPARC,APF, DAB, Zic, Pax6, Flk1 or CD31) or for identification of cells whichdo not express these negative markers (e.g. definitive endoderm cells).A reagent for a marker can be, for example, an antibody against themarker or primers for a RT-PCR or PCR reaction, e.g., asemi-quantitative or quantitative RT-PCR or PCR reaction. Such markerscan be used to evaluate whether a definitive endoderm cell has beenproduced. The antibody or other detection reagent can be linked to alabel, e.g., a radiological, fluorescent (e.g., GFP) or colorimetriclabel for use in detection. If the detection reagent is a primer, it canbe supplied in dry preparation, e.g., lyophilized, or in a solution.

The progression of a pluripotent stem cell to a definitive endoderm canbe monitored by determining the expression of markers characteristic ofdefinitive endoderm cells. In some processes, the expression of certainmarkers is determined by detecting the presence or absence of themarker. Alternatively, the expression of certain markers can bedetermined by measuring the level at which the marker is present in thecells of the cell culture or cell population. In certain processes, theexpression of markers characteristic of definitive endoderm cells aswell as the lack of significant expression of markers characteristic ofthe pluripotent stem cell from which it was derived is determined.

As described in connection with monitoring the production of adefinitive endoderm cell from a pluripotent stem cell, qualitative orsemi-quantitative techniques, such as blot transfer methods andimmunocytochemistry, can be used to measure marker expression, usingmethods commonly known to persons of ordinary skill in the art.Alternatively, marker expression can be accurately quantitated throughthe use of technique such as quantitative-PCR by methods ordinarilyknown in the art. Additionally, it will be appreciated that at thepolypeptide level, many of the markers of pancreatic islethormone-expressing cells are secreted proteins. As such, techniques formeasuring extracellular marker content, such as ELISA, may be utilized.

In other embodiments, the expression of Tmprss2, Tmem30b, St14, Spink3,Sh3gl2, Ripk4, Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb,FoxA1, Fox2A, Sox17 and Rbm35a in a definitive endoderm cell is at leastabout 4-fold higher, at least about 6-fold higher, at least about 8-foldhigher, at least about 10-fold higher, at least about 15-fold higher, atleast about 20-fold higher, at least about 40-fold higher, at leastabout 80-fold higher, at least about 100-fold higher, at least about150-fold higher, at least about 200-fold higher, at least about 500-foldhigher, at least about 750-fold higher, at least about 1000-fold higher,at least about 2500-fold higher, at least about 5000-fold higher, atleast about 7500-fold higher or at least about 10.000-fold higher thanthe expression of Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4,Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Fox2A,Sox17 and Rbm35a in a pluripotent stem cell from which the definitiveendoderm cell was derived.

The chemically induced reprogrammed cells as disclosed herein canexpress any number of pluripotent cell markers, including: Nodal,Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4, Rab15, Npnt, Clic6,Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1 and Rbm35a and other generalmarkers for definitive endoderm cells, etc. Other markers can includethe absence of expression of extra-embryonic endoderm cell markers, suchas but not limited to Gata4, Sparc, AFP and Dab. Other markers includethe absence or expression of Zic, Pax6, Flk1 or CD31. Definitiveendoderm cells can also be characterized by the down-regulation ofmarkers characteristic of the pluripotent stem from which the definitiveendoderm cell is induced from. For example, definitive endoderm cellsderived from pluripotent stem cell may be characterized by astatistically significant down-regulation of the pluripotent stem cellmarkers alkaline phosphatase (AP), NANOG, OCT-4, SOX-2, SSEA4, TRA-1-60or TRA-1-81 in the definitive endoderm relative to the expression in thepluripotent stem cell from which it was derived. Other markers expressedby pluripotent cell markers, include but are not limited to alkalinephosphatase (AP); ABCG2; stage specific embryonic antigen-1 (SSEA-1);SSEA-3; SSEA-4; TRA-1-60; TRA-1-81; Tra-2-49/6E; ERas/ECATS, E-cadherin;.beta.III-tubulin; .alpha.-smooth muscle actin (.alpha.-SMA); fibroblastgrowth factor 4 (Fgf4), Cripto, Dax1; zinc finger protein 296 (Zfp296);N-acetyltransferase-1 (Nat1); (ES cell associated transcript 1 (ECAT1);ESG1/DPPAS/ECAT2; ECAT3; ECAT6; ECAT7; ECAT8; ECAT9; ECAT10; ECAT15-1;ECAT15-2; Fth117; Sa114; undifferentiated embryonic cell transcriptionfactor (Utf1); Rex1; p53; G3PDH; telomerase, including TERT; silent Xchromosome genes; Dnmt3a; Dnmt3b; TRIM28; F-box containing protein 15(Fbx15); Nanog/ECAT4; Oct3/4; Sox2; Klf4; c-Myc; Esrrb; TDGF1; GABRB3;Zfp42, FoxD3; GDF3; CYP25A1; developmental pluripotency-associated 2(DPPA2); T-cell lymphoma breakpoint 1 (Tcl1); DPPA3/Stella; DPPA4;Dnmt3L; Sox15; Stat3; Grb2; SV40 Large T Antigen; HPV16 E6; HPV16 E7,β-catenin, and Bmi1 and other general markers for pluripotency, etc, andat least one or more of these are down regulated by a statisticallysignificant amount in a definitive endoderm cell as compared to thepluripotent stem cell from which they were derived.

It is understood that the present invention is not limited to thosemarkers listed as definitive endoderm markers herein, and the presentinvention also encompasses markers such as cell surface markers,antigens, and other gene products including ESTs, RNA (includingmicroRNAs and antisense RNA), DNA (including genes and cDNAs), andportions thereof. Markers of definitive endoderm can be used, forexample where a definitive endoderm cell expresses at least one markerfrom an endoderm cell. Markers of endoderm cells (which are distinctfrom definitive endoderm cells) include, Gata4, FoxA2, PDX1, Nodal, Sox7and Sox17. By way of completeness, markers of mesoderm cells include,Brachycury, GSC, LEF1, Mox1 and Tie1. Markers of ectoderm cells includecripto1, EN1, GFAP, Islet 1, LIM1 and Nestin. Antibodies to markers ofthe three germ layers are commercially available, such as available fromAbcam and other commercial antibody companies.

In some embodiments, a population of definitive endoderm cells can bereplated or otherwise manipulated to begin another stage ofdifferentiation. In certain circumstances, differentiation ormaintenance of cells may be enhanced if the cells are kept in micromassclusters (for example, 50 to 5,000 cells), so that alpha, beta, anddelta cells can interact directly.

Enrichment and Isolation and Purification of a Definitive Endoderm Cell

Another aspect of the present invention relates to the isolation of apopulation of definitive endoderm cells from a heterogeneous populationof cells, such a mixed population of cells comprising definitiveendoderm cells and pluripotent stem cells from which the definitiveendoderm cells were derived. A population of definitive endodermproduced by any of the above-described processes can be enriched,isolated and/or purified by using any cell surface marker present on thedefinitive endoderm which is not present on the pluripotent stem cellfrom which it was derived. Such cell surface markers are also referredto as an affinity tag which is specific for a definitive endoderm cell.Examples of affinity tags specific for definitive endoderm cells areantibodies, ligands or other binding agents that are specific to amarker molecule, such as a polypeptide, that is present on the cellsurface of a definitive endoderm cell but which is not substantiallypresent on other cell types (e.g. on pluripotent stem cells). In someprocesses, an antibody which binds to a cell surface antigen on adefinitive endoderm (e.g. a human definitive endoderm cell) is used asan affinity tag for the enrichment, isolation or purification ofchemically induced (e.g. by contacting with a compound Formula I, e.g.IDE1 and/or IDE2) definitive endoderm cells produced by the methodsdescribed herein. Such antibodies are known and commercially available.

The skilled artisan will readily appreciate that the processes formaking and using antibodies for the enrichment, isolation and/orpurification of definitive endoderm cells are also readily adaptable forthe enrichment, isolation and/or purification of definitive endodermcells. For example, in some embodiments, the reagent, such as anantibody, is incubated with a cell population comprising definitiveendoderm cells, wherein the cell population has been treated to reduceintercellular and substrate adhesion. The cell population are thenwashed, centrifuged and resuspended. In some embodiments, if theantibody is not already labeled with a label, the cell suspension isthen incubated with a secondary antibody, such as an FITC-conjugatedantibody that is capable of binding to the primary antibody. Thedefinitive endoderm cells are then washed, centrifuged and resuspendedin buffer. The definitive endoderm cell suspension is then analyzed andsorted using a fluorescence activated cell sorter (FACS).Antibody-bound, fluorescent reprogrammed cells are collected separatelyfrom non-bound, non-fluorescent cells (e.g. non-definitive endodermcells), thereby resulting in the isolation of definitive endoderm cellsfrom pluripotent stem cells or non-definitive endoderm cells (e.g.endoderm cells or differentiated cell types).

In another embodiments of the processes described herein, the isolatedcell composition comprising definitive endoderm cells can be furtherpurified by using an alternate affinity-based method or by additionalrounds of sorting using the same or different markers that are specificfor definitive endoderm cells. For example, in some embodiments, FACSsorting is used to first isolate a definitive endoderm cell whichexpresses at least one of: Sox17 or Fox2A (HNF3β), either alone or witha marker selected from the group of Nodal, Tmprss2, Tmem30b, St14,Spink3, Sh3gl2, Ripk4, Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4,Emb, FoxA1, Fox2A, Sox17 and Rbm35a from cells that do not express oneof those markers (e.g. negative cells) in the cell population. A secondFAC sorting, e.g. sorting the positive cells again using FACS to isolatecells that are positive for a different marker than the first sort (e.g.selecting for cells which are positive for at least one of: Sox17 orFox2A (HNF3β) or Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4,Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Fox2A,Sox17 and Rbm35a, where the selected marker is different to the firstsort) enriches the cell population for reprogrammed cells.

In an alternative embodiment, FACS sorting is used to separate cells bynegatively sorting for a marker that is present on most pluripotent stemcells, or a marker which not present on the definitive endoderm cells.For example, one can negatively select for cells which express at leastone of Gata4, SPARC, APF or DAB, or Zic, Pax6, Flk1 or CD31 and discardthese cells which express Gata4, SPARC, APF, DAB, Zic, Pax6, Flk1 orCD31 and collect the cells which have negative expression of at leastone of Gata4, SPARC, APF, DAB, Zic, Pax6, Flk1 r CD31.

In some embodiments of the processes described herein, definitiveendoderm cells are fluorescently labeled without the use of an antibodythen isolated from non-labeled cells by using a fluorescence activatedcell sorter (FACS). In such embodiments, a nucleic acid encoding GFP,YFP or another nucleic acid encoding an expressible fluorescent markergene, such as the gene encoding luciferase, is used to labelreprogrammed cells using the methods described above. For example, insome embodiments, at least one copy of a nucleic acid encoding GFP or abiologically active fragment thereof is introduced into a pluripotentstem cell which is to be chemically induced into a definitive endodermcell, where a downstream of a promoter expressed in a definitiveendoderm cell, such as the Sox17 promoter, such that the expression ofthe GFP gene product or biologically active fragment thereof is undercontrol of the Sox17 promoter. In some embodiments, the entire codingregion of the nucleic acid, which encodes Sox17 is replaced by a nucleicacid encoding GFP or a biologically active fragment thereof. In otherembodiments, the nucleic acid encoding GFP or a biologically activefragment thereof is fused in frame with at least a portion of thenucleic acid encoding Sox17, thereby generating a fusion protein. Insuch embodiments, the fusion protein retains a fluorescent activitysimilar to GFP.

In addition to the procedures just described, chemically induceddefinitive endoderm cells may also be isolated by other techniques forcell isolation. Additionally, definitive endoderm cells may also beenriched or isolated by methods of serial subculture in growthconditions which promote the selective survival or selective expansionof the definitive endoderm cells. Such methods are known by persons ofordinary skill in the art.

Using the methods described herein, enriched, isolated and/or purifiedpopulations of definitive endoderm cells can be produced in vitro frompluripotent stem cells. Some preferred enrichment, isolation and/orpurification methods relate to the in vitro production of humandefinitive endoderm cells from human pluripotent stem cells, or fromhuman induced pluripotent stem (iPS) cells. In such an embodiment, wheredefinitive endoderm cells are derived from iPS cells, the definitiveendoderm cells can be autologous to the subject from whom the cells wereobtained to generate the iPS cells.

Using the methods described herein, isolated cell populations ofdefinitive endoderm cells are enriched in definitive endoderm content byat least about 2- to about 1000-fold as compared to a population ofcells before the chemical induction of a pluripotent stem cellpopulation. In some embodiments, definitive endoderm cells can beenriched by at least about 5- to about 500-fold as compared to apopulation before the chemical induction of a pluripotent stem cellpopulation. In other embodiments, definitive endoderm cells can beenriched from at least about 10- to about 200-fold as compared to apopulation before the chemical induction of a pluripotent stem cellpopulation. In still other embodiments, definitive endoderm cells can beenriched from at least about 20- to about 100-fold as compared to apopulation before the chemical induction of a pluripotent stem cellpopulation. In yet other embodiments, definitive endoderm cells can beenriched from at least about 40- to about 80-fold as compared to apopulation before the chemical induction of a pluripotent stem cellpopulation. In certain embodiments, definitive endoderm cells can beenriched from at least about 2- to about 20-fold as compared to apopulation before the chemical induction of a pluripotent stem cellpopulation.

Compositions Comprising Definitive Endoderm Cells

Some embodiments of the present invention relate to cell compositions,such as cell cultures or cell populations, comprising definitiveendoderm cells, wherein the definitive endoderm cells which have beenderived from pluripotent stem cells e.g. human pluripotent stem cells.In accordance with certain embodiments, the chemically induceddefinitive endoderm cells are mammalian cells, and in a preferredembodiment, such definitive endoderm cells are human definitive endodermcells.

Other embodiments of the present invention relate to compositions, suchas an isolated cell population or cell culture, comprising definitiveendoderm cells produced by the methods as disclosed herein. In someembodiments of the present invention relate to compositions, such asisolated cell populations or cell cultures, comprisingchemically-induced definitive endoderm cells produced by the methods asdisclosed herein. In such embodiments, the definitive endoderm cellscomprise less than about 90%, less than about 85%, less than about 80%,less than about 75%, less than about 70%, less than about 65%, less thanabout 60%, less than about 55%, less than about 50%, less than about45%, less than about 40%, less than about 35%, less than about 30%, lessthan about 25%, less than about 20%, less than about 15%, less thanabout 12%, less than about 10%, less than about 8%, less than about 6%,less than about 5%, less than about 4%, less than about 3%, less thanabout 2% or less than about 1% of the total cells in the definitiveendoderm cell population. In some embodiments, the composition comprisesa population of definitive endoderm cells which make up more than about90% of the total cells in the cell population, for example about atleast 95%, or at least 96%, or at least 97%, or at least 98% or at leastabout 99%, or about at least 100% of the total cells in the cellpopulation are definitive endoderm cells.

Certain other embodiments of the present invention relate tocompositions, such as an isolated cell population or cell cultures,comprise a combination of definitive endoderm cells and the pluripotentstem cells from which the definitive endoderm cells were derived. Insome embodiments, the pluripotent stem cells from which the definitiveendoderm cells are derived comprise less than about 25%, less than about20%, less than about 15%, less than about 10%, less than about 5%, lessthan about 4%, less than about 3%, less than about 2% or less than about1% of the total cells in the isolated cell population or culture.

Additional embodiments of the present invention relate to compositions,such as isolated cell populations or cell cultures, produced by theprocesses described herein and which comprise chemically induceddefinitive endoderm cells as the majority cell type. In someembodiments, the methods and processes described herein produces anisolated cell culture and/or cell populations comprising at least about99%, at least about 98%, at least about 97%, at least about 96%, atleast about 95%, at least about 94%, at least about 93%, at least about92%, at least about 91%, at least about 90%, at least about 89%, atleast about 88%, at least about 87%, at least about 86%, at least about85%, at least about 84%, at least about 83%, at least about 82%, atleast about 81%, at least about 80%, at least about 79%, at least about78%, at least about 77%, at least about 76%, at least about 75%, atleast about 74%, at least about 73%, at least about 72%, at least about71%, at least about 70%, at least about 69%, at least about 68%, atleast about 67%, at least about 66%, at least about 65%, at least about64%, at least about 63%, at least about 62%, at least about 61%, atleast about 60%, at least about 59%, at least about 58%, at least about57%, at least about 56%, at least about 55%, at least about 54%, atleast about 53%, at least about 52%, at least about 51% or at leastabout 50% definitive endoderm cells.

In another embodiment, isolated cell populations or compositions ofcells (or cell cultures) comprise human definitive endoderm cells. Inother embodiments, the methods and processes as described herein canproduce isolated cell populations comprising at least about 50%, atleast about 45%, at least about 40%, at least about 35%, at least about30%, at least about 25%, at least about 24%, at least about 23%, atleast about 22%, at least about 21%, at least about 20%, at least about19%, at least about 18%, at least about 17%, at least about 16%, atleast about 15%, at least about 14%, at least about 13%, at least about12%, at least about IT %, at least about 10%, at least about 9%, atleast about 8%, at least about 7%, at least about 6%, at least about 5%,at least about 4%, at least about 3%, at least about 2% or at leastabout 1% definitive endoderm cells. In preferred embodiments, isolatedcell populations can comprise human definitive endoderm cells. In someembodiments, the percentage of definitive endoderm cells in the cellcultures or populations is calculated without regard to the feeder cellsremaining in the culture.

Still other embodiments of the present invention relate to compositions,such as isolated cell populations or cell cultures, comprising mixturesof definitive endoderm cells and pluripotent stem cells. For example,cell cultures or cell populations comprising at least about 5 definitiveendoderm cells for about every 95 pluripotent stem cell can be produced.In other embodiments, cell cultures or cell populations comprising atleast about 95 definitive endoderm cells for about every 5 pluripotentstem cell can be produced. Additionally, cell cultures or cellpopulations comprising other ratios of definitive endoderm cells topluripotent stem cells are contemplated. For example, compositionscomprising at least about 1 definitive endoderm cell for about every1,000,000, or at least 100,000 cells, or a least 10,000 cells, or atleast 1000 cells or 500, or at least 250 or at least 100 or at least 10pluripotent stem cell can be produced.

Further embodiments of the present invention relate to compositions,such as cell cultures or cell populations, comprising human cells,including human definitive endoderm cells which express Sox17 and atleast two or at least 3 or more characteristics of a cell of adefinitive endoderm cell, such as FoxA2 (HNF3β) or do not express Gata4,Sparc, Apf or Dab.

In preferred embodiments of the present invention, cell cultures and/orcell populations of definitive endoderm cells comprise human definitiveendoderm cells, that are non-recombinant cells. In such embodiments, thecell cultures and/or cell populations are devoid of or substantiallyfree of recombinant human definitive endoderm cells.

Use of the Definitive Endoderm Cells

Another aspect relates to the use of the definitive endoderm cellsproduced by the methods as disclosed herein for subsequentdifferentiating into a Pdx1-positive progenitor cell.

In some embodiments, an endoderm cell, e.g., a definitive endoderm cellproduced by a method described herein, is differentiated to a cell of asecond cell type (e.g., a differentiated cell). Included herein arecells and compositions made by the methods described herein. Exemplarysecond cell types include those cells which are derived from endodermsuch as liver, lung, stomach, intestine, and thymus as well as thepancreas. For example, in some embodiments, definitive endoderm cellsmay be differentiated into liver endoderm cells by contacting thedefinitive endoderm cell with about 10 ng/ml-100 ng/ml (preferably,about 50 ng/ml) of FGF10.

In some embodiments, an endoderm cell, e.g., a definitive endoderm cellproduced by a method described herein, is differentiated into apancreatic cell, such as, for example, pancreatic endocrine cells (alphacells, β-cells, delta cells, Pdx1-positive pancreatic progenitors (alsoreferred to herein as “PP” cells) and the like) or a pancreatic exocrinecell.

In certain embodiments, the definitive endoderm cells produced by themethods as disclosed herein are produced from the human or mousepluripotent stem cells, e.g. embryonic stem cells. Pancreatic cellprecursors, e.g. Pdx1-positive progenitors can be differentiatedfurther, either in a single step or in multiple steps, to ainsulin-producing cells.

In accordance with certain examples, step-wise differentiation may beimplemented to differentiate stem cells to a desired cell, such as apancreatic cell. One method of step-wise differentiation is described inU.S. Pat. No. 7,326,572, which is incorporated herein in its entirety byreference. In brief, a pluripotent stem cell population isdifferentiated into a definitive endoderm cell using the methods asdisclosed herein, and then further differentiated into a pdx1-positivepancreatic progenitor using the methods as disclosed herein, which canoptionally be further differentiated into more mature cells that aremore and more specialized towards the formation of certain types ofpancreatic cells, such as towards insulin producing cells such aspancreatic β-cells. Using this step-wise differentiation, pluripotentstem cells, e.g. hESC or iPS cells can be differentiated toward a maturepancreatic cell type in several deliberate stages.

In certain embodiments, an immature endoderm cells, e.g. definitiveendoderm cells may first be produced from undifferentiated stem cells.For examples, early in ontogeny, endoderm cells are capable of makingepithelial cells of the GI tract and respiratory system, and the keydigestive organs (liver and pancreas). Pancreatic cells can begenerated, for example, using a two-stage approach. Stage 1 generallyinvolves obtaining a population of common endoderm precursor cells.Stage 2 generally involves maturing the endoderm precursors into thepancreatic cells such as, for example, beta cells. In certainembodiments disclosed herein, the common endoderm precursor cells may bedifferentiated to provide pancreatic cell precursors such as, forexample, Pdx1⁺ pancreatic cell precursors.

Stem cells can also be differentiated along the endoderm differentiationpathway by culturing with the suitable agents such as, for examples, thehepatocyte differentiation agent n-butyrate. A further description ofthe hepatocyte differentiation paradigm may be found in InternationalPatent Publication WO 01/81549 (Geron Corporation) which is incorporatedherein by reference. Sonic Hedgehog is thought to be involved in liverspecification, so including cyclopamine (an inhibitor of Sonic Hedgehog)in the culture medium is thought to help divert the cells toward thepancreatic lineage.

In some examples, differentiation of pdx1-positive progenitors mayfurther be directed in a subsequent step, using, for example, theterminal differentiation factor nicotinamide (in the presence ofcyclopamine and activin A). In other examples, one or more additionalstages of differentiation may be implemented. For example, it may bedesirable to further differentiate or mature of the pancreatic cellsinto a desired cell type.

In certain embodiments disclosed herein, the stem cells may be culturedor exposed to one or more compounds described herein during any one ormore stages of the step-wise differentiation. For example, it may bedesirable to expose undifferentiated hESCs to at least one compounddescribed herein during the first stage of the step-wisedifferentiation, the second stage of step-wise differentiation and/orany additional stages of step-wise differentiation. In other examples,it may be desirable to expose the stem cells to at least one compounddescribed herein only after the first stage of step-wisedifferentiation.

In certain examples, the desired number of stages for producingpancreatic cell types may be based, at least in part, on the intendeduse of the end-stage cell populations. For example, it may be desirableto produce beta cell precursors for therapy for treating metabolicdisorders. In other examples, it may be desirable to furtherdifferentiate the pdx1-positive pancreatic progenitors intoinsulin-producing cells or pancreatic β-cells or pancreatic β-like cellsfor use in treating diabetes.

Another embodiments relate to the use of a definitive endoderm cells fortransplanting into a subject in need thereof, where the definitiveendoderm cell differentiates in vivo into a insulin-producing cell suchas a pancreatic β-cell or pancreatic β-like cell.

Another aspect relates to the use of the Pdx1-positive pancreaticprogenitor cells produced by the methods as disclosed herein forsubsequent differentiating into insulin-producing cells, such aspancreatic β-cells or pancreatic β-like cells.

Another embodiments relate to the use of a Pdx1-positive pancreaticprogenitor cells for transplanting into a subject in need thereof, wherea Pdx1-positive pancreatic progenitor cell can spontaneouslydifferentiate in vivo into a insulin-producing cell such as a pancreaticβ-cell or pancreatic β-like cells.

Compounds for Inducing the Differentiation of Definitive Endoderm Cellsinto a Pdx1-Positive Progenitor

One aspect of the present invention provides methods of producing aPdx1-positive pancreatic progenitor cell, by contacting (e.g.,culturing) an endoderm cell, e.g. a definitive endoderm cell with acompound of Formula (II) as described herein. Accordingly, in someembodiments any compound with Formula (II) useful in the methods andcompositions as disclosed herein are cell permeable small molecules, andcan control cellular processes by modulating signal transductionpathways, gene expression or metabolism and have been effectively usedin stem cell differentiation protocols. As discussed previously, smallmolecules of Formula (I) or Formula (II) can be synthesized in highquantity and purity as well as conveniently supplied or removed, givingthem great potential to be useful for therapeutic applications. Highthroughput screens have been performed to identify novel small moleculesthat can support the self renewal of ES cells (Chen et al., 2006;Desbordes et al., 2008), cardiogenic specification of mouse ES cells (Wuet al., 2004) or neural progenitor cells (Diamandis et al., 2007) aswell as inducing specific cell types, notably neuronal and muscle cells(reviewed by (Ding and Schultz, 2004).

In one embodiment, an endoderm cell, e.g. a definitive endoderm cell,such as a human endoderm cell, or a human cell of endoderm origin iscontacted with at least one compound of Formula (II) to differentiatethe endoderm cell, e.g. a definitive endoderm cell into a Pdx1-positiveprogenitor cell.

In some embodiments, the method further comprises contacting apopulation of definitive endoderm cells with at least one compound ofFormula (II) to induce differentiation of at least one definitiveendoderm cell into a Pdx1-positive pancreatic progenitor cell, whereinthe compound of Formula (II) is:

-   R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or    cyclyl, each of which can be optionally substituted;-   R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl,    alkynyl, alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which    can be optionally substituted; and-   R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl,    alkenyl, alkynyl, alkoxy, thioalkyl, aryl, heteroaryl, cyclyl, or    cyclyl, each of which can be optionally substituted, or R²⁴ and R²⁵    together with the carbons to which they arre attached form an    optionally substituted cyclyl.

In some embodiments, the compound of formula (II) has the structureshown in formula (III):

In some other embodiments, the compound of formula (II) has thestructure shown in formula (IV):

In some embodiments, R²¹ is C₁-C₆alkyl. Preferably R²¹ is methyl orethyl. Most preferably R²¹ is methyl.

In some embodiments, R²² is C₁-C₆alkyl. Preferably R²² is methyl, ethyl,propyl, or isopropyl. Most preferably, R²² is isopropyl.

In some embodiments, R²³ is a substituted C₁-C₆ alkyl. Preferably R²² issubstituted with a hydroxyl group. In one preferred embodiment, R²³ ishydroxymethyl.

In some embodiments, R²⁴ is hydrogen, halogen, or optionally substitutedlinear or branched alkyl. Preferably R²⁴ is hydrogen.

In some embodiments, R²⁵ is an optionally substituted linear or branchedalkyl, alkenyl or alkynyl. Generally, R²⁵ comprises can comprise one ormore isoprenoid structure. Preferably R²⁵ comprises 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, or 20 carbon atoms.

Preferred compounds of formula (II) include, but are not limited to,(2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((−)-indolactam V),(2R,5R)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one((+)-indolactam V), (−)-7-octylindolactam V, (+)-7-octylindolactam V,and teleocidins (e.g., teleocidin A1, teleocidin A2, telecidin B1,telecidin B2, teleocidin B3, teleocidin B4 (Olivoretin D), anddihydrotelecidin B3).

In some embodiments of this aspect of the present invention providesmethods of producing a Pdx1-positive pancreatic progenitor cell, bycontacting (e.g., culturing) an endoderm cell, e.g. a definitiveendoderm cell with a compound of Formula (II) as described herein,wherein the a cell of definitive endoderm is contacted with a compoundof Formula (II) of about between 20 nM to 5 μM, or between about 20 nMto 50 nM, or about 50 nM to 100 nM, or about 100 nM to 200 nM, or about200 nM to about 500 nM or about 500 nM to about 1 μM, or about 1 μM to 2μm, or about 2 μM to 4 μm, or about 2 μM to 5 μM.

In some embodiments of this aspect of the present invention providesmethods of producing a Pdx1-positive pancreatic progenitor cell, bycontacting (e.g., culturing) an endoderm cell, e.g. a definitiveendoderm cell with a compound of Formula (II) as described herein,wherein the a cell of definitive endoderm is contacted with indolactam-V(ILV) at a concentration of at least about 5 nM, at least about 7 nM, atleast about 10 nM, at least about 12 nM, at least about 15 nM, at leastabout 17 nM, at least about 20 nM, at least about 25 nM, at least about30 nM, at least about 35 nM, at least about 40 nM, at least about 45 nM,at least about 50 nM, at least about 100 nM or at least about 200 nM, orat least about 300 nM or at least about 400 nM or at least about 500 nMor more than 500 nM, or any inter between 10-500 nM or any inter between5-50 nM, or any integer between 50-100 nM, or any integer between 100nM-200 nM or any interger between 200 nM-500 nM. In some embodiments, adefinitive endoderm cell is contacted with indolatcam V at aconcentration of at least about 0.1 μM, or at least about 0.2 μM, or atleast about 0.3 μM, or at least about 0.4 μM, or at least about 0.5 μM,or at least about 1 μM, at least about 1.5 μM, at least about 2 μM, atleast about 2.5 μM, at least about 3 μM, at least about 3.5 μM, at leastabout 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 6μM, at least about 7 μM, at least about 8 μM, at least about 9 μM, or atleast about 10 μM, or more than 10 μM, or any inter between 0.1-0.5 μMor any integer between about 0.5-10 μM or any inter between 0.1-10 μM,or any integer between 0.5-5 μM, or any integer between 5 μM-10 μM. Insome embodiments, a definitive endoderm cell is contacted withindolatcam V at a concentration of about 300 nM to differentiate thedefinitive endoderm cell into a Pdx1-positive pancreatic precursor cell.

Pdx1-Positive Pancreatic Progenitor Produced from Endoderm Cells

One can use any means common to one of ordinary skill in the art toconfirm the presence of a Pdx1-positive pancreatic progenitor cell, e.g.a Pdx1-positive pancreatic progenitor cell produced the induction of thedifferentiation of a definitive endoderm cell by exposure to a compoundof Formula (II), e.g. as indolatam V (ILV). In some embodiments, thepresence of endoderm cells can be detected using suitable markers suchas those listed in International Patent No. WO/2009/132083, which isincorporated herein in its entirety by reference.

In some embodiments, the presence of Pdx1-positive pancreatic progenitormarkers, e.g. chemically induced Pdx1-positive pancreatic progenitorcells can be done by detecting the presence or absence of one or moremarkers indicative of an Pdx1-positive pancreatic progenitor. In someembodiments, the method can include detecting the positive expression(e.g. the presence) of a marker for Pdx1-positive pancreatic progenitorcells. In some embodiments, the marker can be detected using a reagent,e.g., a reagent for the detection of Pdx1. In particular, Pdx1-positivepancreatic progenitors herein express Pdx1 and HNF6. Other positivemarkers for Pdx1-positive pancreatic progenitor cells also include, forexample as shown FIG. 4C of WO2009/132083, which include Pdx1, HNF6,PFT1A, Sox9, FoxA2, Ngn3, Nkx2.2 and Nkx6.1. Negative markers (e.g. theabsence of significant levels of expression) for Pdx1-positivepancreatic progenitor cells include Sox7, Cdx2, Ces2, Fabp2, AFP,Albumlin, Barx1, Troponin and Sox2. Further, similar to definitiveendoderm cells, Pdx1-positive pancreatic progenitor do not expressextra-embryonic (EE) endoderm markers such as Gata4, SPARC, APF and DAB,or negative markers Zic, Pax6, Flk1 or CD31. Also encompassed is thenegative expression of definitive endoderm markers, such as Sox17 andFoxA2 (HNF3β). Negative markers of Pdx1-positive pancreatic progenitorcells are useful for the purposes of negative selection ofnon-Pdx1-positive pancreatic progenitor cells (e.g. selection anddiscarding cells which express Gata4, SPARC, APF, DAB, Zic, Pax6, Flk1or CD31) or for identification of cells which do not express thesenegative markers (e.g. Pdx1-positive pancreatic progenitor cells). Areagent for a marker can be, for example, an antibody against the markeror primers for a RT-PCR or PCR reaction, e.g., a semi-quantitative orquantitative RT-PCR or PCR reaction. Such markers can be used toevaluate whether a definitive endoderm cell has been produced. Theantibody or other detection reagent can be linked to a label, e.g., aradiological, fluorescent (e.g., GFP) or colorimetric label for use indetection. If the detection reagent is a primer, it can be supplied indry preparation, e.g., lyophilized, or in a solution.

The progression of the differentiation of a definitive endoderm to aPdx1-positive pancreatic progenitor can be monitored by determining theexpression of markers characteristic of Pdx1-positive pancreaticprogenitor cells. In some processes, the expression of certain markersis determined by detecting the presence or absence of the marker.Alternatively, the expression of certain markers can be determined bymeasuring the level at which the marker is present in the cells of thecell culture or cell population. In certain processes, the expression ofmarkers characteristic of Pdx1-positive pancreatic progenitor cells aswell as the lack of significant expression of markers characteristic ofthe definitive endoderm cells from which it was derived is determined.

As described in connection with monitoring the production of aPdx1-positive pancreatic progenitor from a definitive endoderm cell,qualitative or semi-quantitative techniques, such as blot transfermethods and immunocytochemistry, can be used to measure markerexpression, using methods commonly known to persons of ordinary skill inthe art. Alternatively, marker expression can be accurately quantitatedthrough the use of technique such as quantitative-PCR by methodsordinarily known in the art. Additionally, it will be appreciated thatat the polypeptide level, many of the markers of pancreatic islethormone-expressing cells are secreted proteins. As such, techniques formeasuring extracellular marker content, such as ELISA, may be utilized.

In other embodiments, the expression of Pdx1 or Cdcp1, or Ptf1a, or HNF6or Nkx2.2 in a Pdx1-positive pancreatic progenitor cell is at leastabout 4-fold higher, at least about 6-fold higher, at least about 8-foldhigher, at least about 10-fold higher, at least about 15-fold higher, atleast about 20-fold higher, at least about 30-fold higher, at leastabout 40-fold higher, at least about 50-fold higher, at least about60-fold higher, at least about 70-fold higher, at least about 80-foldhigher, at least about 90-fold higher, at least about 100-fold higher ormore than 100-fold higher than the expression of Pdx1 or Cdcp1, orPtf1a, or HNF6 or Nkx2.2 in a definitive endoderm cell or pluripotentstem cell from which the Pdx1-positive pancreatic progenitor cell wasderived.

The chemically induced reprogrammed cells as disclosed herein canexpress any number of Pdx1-positive pancreatic progenitor, including:Pdx1 or Cdcp1, or Ptf1a, or HNF6 or Nkx2.2 or Fox2A and other generalmarkers for Pdx1-positive pancreatic progenitor cells, etc. Othermarkers can include the absence of expression of extra-embryonicendoderm cell markers, such as but not limited to Gata4, Sparc, AFP andDab. Other markers include the absence or expression of Zic, Pax6, Flk1or CD31. Definitive endoderm cells can also be characterized by thedown-regulation of markers characteristic of non-pancreatic lineages,such as Sox7, Cdx2, Ces2, Fabp2, AFP, Albumlin, Barx1, Troponin andSox2.

It is understood that the present invention is not limited to thosemarkers listed as Pdx1-positive pancreatic progenitor markers herein,and the present invention also encompasses markers such as cell surfacemarkers, antigens, and other gene products including ESTs, RNA(including microRNAs and antisense RNA), DNA (including genes andcDNAs), and portions thereof.

In some embodiments, a population of Pdx1-positive pancreatic progenitorcan be replated or otherwise manipulated to begin another stage ofdifferentiation. In certain circumstances, differentiation ormaintenance of cells may be enhanced if the cells are kept in micromassclusters (for example, 50 to 5,000 cells), so that alpha, beta, anddelta cells can interact directly.

Enrichment and Isolation and Purification of a Pdx1-Positive PancreaticProgenitor Cell

Another aspect of the present invention relates to the isolation of apopulation of Pdx1-positive pancreatic progenitor cells from aheterogeneous population of cells, such a mixed population of cellscomprising Pdx1-positive pancreatic progenitor cells and definitiveendoderm cells from which the Pdx1-positive pancreatic progenitor cellswere derived. A population of Pdx1-positive pancreatic progenitorproduced by any of the above-described processes can be enriched,isolated and/or purified by using any cell surface marker present on thePdx1-positive pancreatic progenitor which is not present on thedefinitive endoderm cell from which it was derived. Such cell surfacemarkers are also referred to as an affinity tag which is specific for aPdx1-positive pancreatic progenitor cell. Examples of affinity tagsspecific for Pdx1-positive pancreatic progenitor cells are antibodies,ligands or other binding agents that are specific to a marker molecule,such as a polypeptide, that is present on the cell surface of aPdx1-positive pancreatic progenitor cell but which is not substantiallypresent on other cell types (e.g. on definitive endoderm cells). In someprocesses, an antibody which binds to a cell surface antigen on aPdx1-positive pancreatic progenitor (e.g. a human Pdx1-positivepancreatic progenitor cell) is used as an affinity tag for theenrichment, isolation or purification of chemically induced (e.g. bycontacting with a compound Formula II, e.g. indolactam V (ILV))Pdx1-positive pancreatic progenitor cells produced by the methodsdescribed herein. Such antibodies are known and commercially available.

The skilled artisan will readily appreciate that the processes for usingantibodies for the enrichment, isolation and/or purification ofPdx1-positive pancreatic progenitor cells. For example, in someembodiments, the reagent, such as an antibody, is incubated with a cellpopulation comprising Pdx1-positive pancreatic progenitor cells, whereinthe cell population has been treated to reduce intercellular andsubstrate adhesion. The cell population are then washed, centrifuged andresuspended. In some embodiments, if the antibody is not already labeledwith a label, the cell suspension is then incubated with a secondaryantibody, such as an FITC-conjugated antibody that is capable of bindingto the primary antibody. The Pdx1-positive pancreatic progenitor cellsare then washed, centrifuged and resuspended in buffer. ThePdx1-positive pancreatic progenitor suspension is then analyzed andsorted using a fluorescence activated cell sorter (FACS).Antibody-bound, fluorescent reprogrammed cells are collected separatelyfrom non-bound, non-fluorescent cells (e.g. non-Pdx1-positive pancreaticprogenitors), thereby resulting in the isolation of Pdx1-positivepancreatic progenitors from other cells present in the cell suspension,e.g. definitive endoderm cells, pluripotent stem cells ornon-Pdx1-positive pancreatic progenitors (e.g. other differentiated celltypes).

In another embodiments of the processes described herein, the isolatedcell composition comprising Pdx1-positive pancreatic progenitor cellscan be further purified by using an alternate affinity-based method orby additional rounds of sorting using the same or different markers thatare specific for Pdx1-positive pancreatic progenitors. For example, insome embodiments, FACS sorting is used to first isolate a Pdx1-positivepancreatic progenitor which expresses Pdx1, either alone or with theexpression of HNF6, or alternatively with a marker selected from thegroup of Cdcp1, Ptf1a, Fox2A, Pdx1, Sox9, FoxA2, Ngn3, Nkx2.2 and Nkx6.1from cells that do not express one of those markers (e.g. negativecells) in the cell population. A second FAC sorting, e.g. sorting thepositive cells again using FACS to isolate cells that are positive for adifferent marker than the first sort (e.g. selecting for cells which arepositive for at least one of: Cdcp1, Ptf1a, Fox2A, Pdx1, Sox9, FoxA2,Ngn3, Nkx2.2 and Nkx6. where the selected marker is different to thefirst sort) enriches the cell population for reprogrammed cells.

In an alternative embodiment, FACS sorting is used to separate cells bynegatively sorting for a marker that is present on most definitiveendoderm cells but is not present on Pdx1-positive pancreatic progenitorcells. For example, one can negatively select for cells which express atleast one of Gata4, SPARC, APF or DAB, or Zic, Pax6, Flk1 or CD31 anddiscard these cells which express Sox17, Afp and collect the cells whichhave negative expression of at least one of Sox17, Afp or other negativePdx1-positive pancreatic progenitor cells.

In some embodiments of the processes described herein, Pdx1-positivepancreatic progenitor cells are fluorescently labeled without the use ofan antibody then isolated from non-labeled cells by using a fluorescenceactivated cell sorter (FACS). In such embodiments, a nucleic acidencoding GFP, YFP or another nucleic acid encoding an expressiblefluorescent marker gene, such as the gene encoding luciferase, is usedto label reprogrammed cells using the methods described above. Forexample, in some embodiments, at least one copy of a nucleic acidencoding GFP or a biologically active fragment thereof is introducedinto a pluripotent stem cell which is first chemically induced into adefinitive endoderm cell and then into a Pdx1-positive pancreaticprogenitor, where a downstream of a promoter expressed in aPdx1-positive pancreatic progenitor cell, such as the Pdx1 promoter,such that the expression of the GFP gene product or biologically activefragment thereof is under control of the Pdx1 promoter.

In addition to the procedures just described, chemically inducedPdx1-positive pancreatic progenitor cells may also be isolated by othertechniques for cell isolation. Additionally, Pdx1-positive pancreaticprogenitor cells may also be enriched or isolated by methods of serialsubculture in growth conditions which promote the selective survival orselective expansion of the Pdx1-positive pancreatic progenitor cells.Such methods are known by persons of ordinary skill in the art.

Using the methods described herein, enriched, isolated and/or purifiedpopulations of Pdx1-positive pancreatic progenitor can be produced invitro from definitive endoderm cells (which were differentiated frompluripotent stem cells by the methods described herein). In someembodiments, preferred enrichment, isolation and/or purification methodsrelate to the in vitro production of human Pdx1-positive pancreaticprogenitor from human definitive endoderm cells, which weredifferentiated from human pluripotent stem cells, or from human inducedpluripotent stem (iPS) cells. In such an embodiment, where Pdx1-positivepancreatic progenitor are differentiated from definitive endoderm cellswhich were previously derived from iPS cells, the Pdx1-positivepancreatic progenitor cell can be autologous to the subject from whomthe cells were obtained to generate the iPS cells.

Using the methods described herein, isolated cell populations ofPdx1-positive pancreatic progenitor cells are enriched in Pdx1-positivepancreatic progenitor content by at least about 2- to about 1000-fold ascompared to a population of cells before the chemical induction of thedefinitive endoderm cell population. In some embodiments, Pdx1-positivepancreatic progenitor cells can be enriched by at least about 5- toabout 500-fold as compared to a population before the chemical inductionof a definitive endoderm cell population. In other embodiments,Pdx1-positive pancreatic progenitors can be enriched from at least about10- to about 200-fold as compared to a population before the chemicalinduction of a definitive endoderm cell population. In still otherembodiments, Pdx1-positive pancreatic progenitors can be enriched fromat least about 20- to about 100-fold as compared to a population beforethe chemical induction of a definitive endoderm cell population. In yetother embodiments, Pdx1-positive pancreatic progenitors can be enrichedfrom at least about 40- to about 80-fold as compared to a populationbefore the chemical induction of a definitive endoderm stem cellpopulation. In certain embodiments, Pdx1-positive pancreatic progenitorscan be enriched from at least about 2- to about 20-fold as compared to apopulation before the chemical induction of a definitive endoderm stemcell population.

Compositions Comprising Pdx1-Positive Pancreatic Progenitor Cells

Some embodiments of the present invention relate to cell compositions,such as cell cultures or cell populations, comprising Pdx1-positivepancreatic progenitor cells, wherein the Pdx1-positive pancreaticprogenitor cells have been derived from definitive endoderm cells e.g.human definitive endoderm stem cells. In accordance with certainembodiments, the chemically induced Pdx1-positive pancreatic progenitorsare mammalian cells, and in a preferred embodiment, such Pdx1-positivepancreatic progenitors are human d Pdx1-positive pancreatic progenitors.

Other embodiments of the present invention relate to compositions, suchas an isolated cell population or cell culture, comprising Pdx1-positivepancreatic progenitor cells produced by the methods as disclosed herein.In some embodiments of the present invention relate to compositions,such as isolated cell populations or cell cultures, comprisingchemically-induced Pdx1-positive pancreatic progenitor cells produced bythe methods as disclosed herein. In such embodiments, the Pdx1-positivepancreatic progenitor cells comprise less than about 90%, less thanabout 85%, less than about 80%, less than about 75%, less than about70%, less than about 65%, less than about 60%, less than about 55%, lessthan about 50%, less than about 45%, less than about 40%, less thanabout 35%, less than about 30%, less than about 25%, less than about20%, less than about 15%, less than about 12%, less than about 10%, lessthan about 8%, less than about 6%, less than about 5%, less than about4%, less than about 3%, less than about 2% or less than about 1% of thetotal cells in the Pdx1-positive pancreatic progenitor population. Insome embodiments, the composition comprises a population ofPdx1-positive pancreatic progenitor cells which make up more than about90% of the total cells in the cell population, for example about atleast 95%, or at least 96%, or at least 97%, or at least 98% or at leastabout 99%, or about at least 100% of the total cells in the cellpopulation are Pdx1-positive pancreatic progenitors.

Certain other embodiments of the present invention relate tocompositions, such as an isolated cell population or cell cultures,comprise a combination of Pdx1-positive pancreatic progenitors anddefinitive endoderm cells from which the Pdx1-positive pancreaticprogenitor were derived. In some embodiments, the definitive endodermcells from which the Pdx1-positive pancreatic progenitor are derivedcomprise less than about 25%, less than about 20%, less than about 15%,less than about 10%, less than about 5%, less than about 4%, less thanabout 3%, less than about 2% or less than about 1% of the total cells inthe isolated cell population or culture.

Additional embodiments of the present invention relate to compositions,such as isolated cell populations or cell cultures, produced by theprocesses described herein and which comprise chemically inducedPdx1-positive pancreatic progenitor as the majority cell type. In someembodiments, the methods and processes described herein produces anisolated cell culture and/or cell populations comprising at least about99%, at least about 98%, at least about 97%, at least about 96%, atleast about 95%, at least about 94%, at least about 93%, at least about92%, at least about 91%, at least about 90%, at least about 89%, atleast about 88%, at least about 87%, at least about 86%, at least about85%, at least about 84%, at least about 83%, at least about 82%, atleast about 81%, at least about 80%, at least about 79%, at least about78%, at least about 77%, at least about 76%, at least about 75%, atleast about 74%, at least about 73%, at least about 72%, at least about71%, at least about 70%, at least about 69%, at least about 68%, atleast about 67%, at least about 66%, at least about 65%, at least about64%, at least about 63%, at least about 62%, at least about 61%, atleast about 60%, at least about 59%, at least about 58%, at least about57%, at least about 56%, at least about 55%, at least about 54%, atleast about 53%, at least about 52%, at least about 51% or at leastabout 50% Pdx1-positive pancreatic progenitor cells.

In another embodiment, isolated cell populations or compositions ofcells (or cell cultures) comprise human Pdx1-positive pancreaticprogenitor cells. In other embodiments, the methods and processes asdescribed herein can produce isolated cell populations comprising atleast about 50%, at least about 45%, at least about 40%, at least about35%, at least about 30%, at least about 25%, at least about 24%, atleast about 23%, at least about 22%, at least about 21%, at least about20%, at least about 19%, at least about 18%, at least about 17%, atleast about 16%, at least about 15%, at least about 14%, at least about13%, at least about 12%, at least about 11%, at least about 10%, atleast about 9%, at least about 8%, at least about 7%, at least about 6%,at least about 5%, at least about 4%, at least about 3%, at least about2% or at least about 1% Pdx1-positive pancreatic progenitor cells. Inpreferred embodiments, isolated cell populations can comprise humanPdx1-positive pancreatic progenitor cells. In some embodiments, thepercentage of Pdx1-positive pancreatic progenitor cells in the cellcultures or populations is calculated without regard to the feeder cellsremaining in the culture.

Still other embodiments of the present invention relate to compositions,such as isolated cell populations or cell cultures, comprising mixturesof Pdx1-positive pancreatic progenitor and definitive endoderm cellsfrom which they were differentiated from. For example, cell cultures orcell populations comprising at least about 5 Pdx1-positive pancreaticprogenitor cells for about every 95 definitive endoderm cell can beproduced. In other embodiments, cell cultures or cell populationscomprising at least about 95 Pdx1-positive pancreatic progenitor cellsfor about every 5 definitive endoderm cell can be produced.Additionally, cell cultures or cell populations comprising other ratiosof Pdx1-positive pancreatic progenitor cells to definitive endodermcells are contemplated. For example, compositions comprising at leastabout 1 Pdx1-positive pancreatic progenitors for about every 1,000,000,or at least 100,000 cells, or a least 10,000 cells, or at least 1000cells or 500, or at least 250 or at least 100 or at least 10 definitiveendoderm cell can be produced.

Further embodiments of the present invention relate to compositions,such as cell cultures or cell populations, comprising human cells,including human Pdx1-positive pancreatic progenitor which express Pdx1and HNF6.

In preferred embodiments of the present invention, cell cultures and/orcell populations of Pdx1-positive pancreatic progenitor cells comprisehuman Pdx1-positive pancreatic progenitor cells, that arenon-recombinant cells. In such embodiments, the cell cultures and/orcell populations are devoid of or substantially free of recombinanthuman Pdx1-positive pancreatic progenitor cells.

Admixture Compositions.

Another aspect of the present invention relates to an admixture ofdefinitive endoderm cells and at least one compound of Formula (I), forexample, compounds IDE1 and/or IDE2 for inducing the differentiation ofpluripotent stem cells to become definitive endoderm cells.

In another aspect of the present invention relates to composition, suchas a reaction admixture comprising a pluripotent stem cell, (e.g. apopulation of pluripotent stem cells for differentiating into definitiveendoderm cells for) and at least one compound of Formula (I).Alternatively, the present invention relates to a reaction admixturecomprising (i) a population of definitive endoderm cells produced bychemical induction of differentiation of a pluripotent stem cell to adefinitive endoderm cell, and (ii) at least one compound of Formula (I),for example but not limited to IDE1 or IDE2.

In some embodiments, the concentrations of a compound of Formula (I)added to the reaction mixture is a sufficient dose for inducing apluripotent stem cell to differentiate into a definitive endoderm cell,as described herein.

In some embodiments, the composition comprises a concentration of acompound of Formula (I) of about between 25 nM to 10 μM, or betweenabout 25 nM to 50 nM, or about 50 nM to 100 nM, or about 100 nM to 200nM, or about 200 nM to about 500 nM or about 500 nM to about 1 μM, orabout 1 μM to 2 μm, or about 2 μM to 5 μm, or about 5 μM to 10 μM.

In some embodiments, a composition or admixture comprises aconcentration of a compound of Formula (I) of at least about 5 nM, atleast about 7 nM, at least about 10 nM, at least about 12 nM, at leastabout 15 nM, at least about 17 nM, at least about 20 nM, at least about25 nM, at least about 30 nM, at least about 35 nM, at least about 40 nM,at least about 45 nM, at least about 50 nM, at least about 100 nM or atleast about 200 nM, or at least about 300 nM or at least about 400 nM orat least about 500 nM or more than 500 nM, or any inter between 10-500nM or any inter between 5-50 nM, or any integer between 50-100 nM, orany integer between 100 nM-200 nM or any integer between 200 nM-500 nM.In some embodiments, a composition or admixture comprises aconcentration of a compound of Formula (I) of at least about 0.1 μM, orat least about 0.2 μM, or at least about 0.3 μM, or at least about 0.4μM, or at least about 0.5 μM, or at least about 1 μM, at least about 1.5μM, at least about 2 μM, at least about 2.5 μM, at least about 3 μM, atleast about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at leastabout 5 μM, at least about 6 μM, at least about 7 μM, at least about 8μM, at least about 9 μM, or at least about 10 μM, or more than 10 μM, orany inter between 0.1-0.5 μM or any integer between about 0.5-10 μM orany inter between 0.1-10 μM, or any integer between 0.5-5 μM, or anyinteger between 5 μM-10 μM.

In some embodiments, a composition or admixture comprises aconcentration of a compound of IDE1 of at least about at least about 20nM, or at least about 25 nM, at least about 30 nM, at least about 35 nM,at least about 40 nM, at least about 45 nM, at least about 50 nM, or atleast about 60 nM, or at least about 70 nM, or at least about 80 nM, orat least about 90 nM, or at least about 100 nM or at least about 200 nM,or at least about 300 nM or at least about 400 nM or at least about 500nM or more than 500 nM, or any inter between 20-500 nM or any interbetween 50-100 nM, or any integer between 50-150 nM, or any integerbetween 100 nM-200 nM or any integer between 200 nM-500 nM. In someembodiments, the composition or admixture comprises a concentration ofIDE1 at about 100 nM.

In some embodiments, a composition or admixture comprises aconcentration of a compound of IDE2 of at least about at least about 20nM, or at least about 25 nM, at least about 30 nM, at least about 35 nM,at least about 40 nM, at least about 45 nM, at least about 50 nM, or atleast about 60 nM, or at least about 70 nM, or at least about 80 nM, orat least about 90 nM, or at least about 100 nM or at least about 200 nM,or at least about 300 nM or at least about 400 nM or at least about 500nM or more than 500 nM, or any inter between 20-500 nM or any interbetween 50-200 nM, or any integer between 100-300 nM, or any integerbetween 100 nM-500 nM or any integer between about 200 nM-500 nM. Insome embodiments, the composition or admixture comprises a concentrationof IDE2 at about 200 nM.

Another aspect of the present invention relates to an admixture ofpdx1-positive pancreatic progenitor cells and at least one compound ofFormula (II), for example, compounds of indolatam-V (ILV) for inducingthe differentiation of a definitive endoderm cells to become apdx1-positive pancreatic progenitor cell.

In another aspect of the present invention relates to composition, suchas a reaction admixture comprising a definitive endoderm cells (e.g.produced by differentiation of a pluripotent stem cell by the methods asdisclosed herein) and at least one compound of Formula (II), such as butnot limited to Indolatam-V (ILV).

In some embodiments, the concentrations of a compound of Formula (I)added to the reaction mixture is a sufficient dose for inducing adefinitive endoderm cell to differentiate into a Pdx1 progenitor asdescribed herein.

In some embodiments, the composition comprises a concentration of acompound of Formula (II) of about between 20 nM to 5 μM, or betweenabout 20 nM to 50 nM, or about 50 nM to 100 nM, or about 100 nM to 200nM, or about 200 nM to about 500 nM or about 500 nM to about 1 μM, orabout 1 μM to 2 μm, or about 2 μM to 4 μm, or about 2 μM to 5 μM.

In some embodiments, a composition or admixture comprises aconcentration of a compound of Formula (II), wherein the compound offormula (II) is indolactam-V (ILV) of at least about 5 nM, at leastabout 7 nM, at least about 10 nM, at least about 12 nM, at least about15 nM, at least about 17 nM, at least about 20 nM, at least about 25 nM,at least about 30 nM, at least about 35 nM, at least about 40 nM, atleast about 45 nM, at least about 50 nM, at least about 100 nM or atleast about 200 nM, or at least about 300 nM or at least about 400 nM orat least about 500 nM or more than 500 nM, or any inter between 10-500nM or any inter between 5-50 nM, or any integer between 50-100 nM, orany integer between 100 nM-200 nM or any integer between 200 nM-500 nM.In some embodiments, a composition or admixture comprises aconcentration of ILV of at least about 0.1 μM, or at least about 0.2 μM,or at least about 0.3 μM, or at least about 0.4 μM, or at least about0.5 μM, or at least about 1 μM, at least about 1.5 μM, at least about 2μM, at least about 2.5 μM, at least about 3 μM, at least about 3.5 μM,at least about 4 μM, at least about 4.5 μM, at least about 5 μM, atleast about 6 μM, at least about 7 μM, at least about 8 μM, at leastabout 9 μM, or at least about 10 μM, or more than 10 μM, or any interbetween 0.1-0.5 μM or any integer between about 0.5-10 μM or any interbetween 0.1-10 μM, or any integer between 0.5-5 μM, or any integerbetween 5 μM-10 μM. In some embodiments, the composition or admixturecomprises a concentration of ILV at about 300 nM.

Compositions and Kits

Described herein are compositions which comprise a cell described herein(e.g., a definitive endoderm cell or a pdx1-positive progenitor cell).In some embodiments, the composition also includes a compound describedherein (e.g., a small molecule such as a compound of formula (I), e.g.,IDE1 and/or IDE2 or an HDAC inhibitor) and/or cell culture media.Described herein are also compositions comprising the compoundsdescribed herein (e.g. cell culture media comprising one or more of thecompounds described herein).Described herein are kits.

Another aspect of the present invention relates to kits for practicingmethods disclosed herein and for making definitive endoderm cellsdisclosed herein. In one aspect, a kit includes a pluripotent stem celland a compound of Formula (I), e.g. but not limited to IDE1 and/or IDE2as described herein, and optionally, the kit can further compriseinstructions for converting a population of pluripotent stem cells to apopulation of definitive endoderm cell using a method described herein.In some embodiments, the kit can further comprise a compound of Formula(II), e.g., but not limited to Indolactam-V (ILV).

In one embodiment, the kit can comprise a pluripotent stem cell for thepurposes of being used as a positive control, for example to assess ormonitor the effectiveness or ability of a compound of formula (I) tochemically induce the pluripotent stem cell to differentiate into adefinitive endoderm cell. Accordingly, the kit can comprise sufficientamount of a compound of Formula (I) for inducing the differentiation ofa control pluripotent stem cell population (positive control) as well asinducing the differentiation of a population of pluripotent stem cellsof interest (e.g. the users preferred pluripotent stem cell e.g. an iPScell) into a population of definitive endoderm cell.

Similarly, the kit can comprise sufficient amount of a compound ofFormula (II) for inducing the differentiation of a control definitiveendoderm cell population (positive control) as well as inducing thedifferentiation of a population of definitive endoderm cells of interest(e.g. the users preferred definitive endoderm cells) into a populationof pdx1-positive pancreatic progenitor cells.

Exemplary components of the kit include the compounds of Formula (I) aredescribed herein, e.g., IDE1 and/or IDE2, and optionally, compound ofFormula (II), e.g. Indolatam-V (ILV).

In some embodiment, the compound in the kit can be provided in awatertight or gas tight container which in some embodiments issubstantially free of other components of the kit. The compound can besupplied in more than one container, e.g., it can be supplied in acontainer having sufficient reagent for a predetermined number ofreactions e.g., 1, 2, 3 or greater number of separate reactions toinduce pluripotent stem cells to definitive endoderm cells, andsubsequently into pdx1-positive endoderm cells. A compound(s) describedherein (e.g., compounds of Formula I or II, such as compounds of Formula(I), including IDE1 and IDE1) or compounds of Formula (II) e.g.Indolactam-V (ILV) can be provided in any form, e.g., liquid, dried orlyophilized form. It is preferred that a compound(s) described herein besubstantially pure and/or sterile. When a compound(s) described hereinis provided in a liquid solution, the liquid solution preferably is anaqueous solution, with a sterile aqueous solution being preferred. Whena compound(s) described herein is provided as a dried form,reconstitution generally is by the addition of a suitable solvent. Thesolvent, e.g., sterile water or buffer, can optionally be provided inthe kit.

In some embodiments, the kit further optionally comprises informationmaterial. The informational material can be descriptive, instructional,marketing or other material that relates to the methods described hereinand/or the use of a compound(s) described herein for the methodsdescribed herein.

The informational material of the kits is not limited in its instructionor informative material. In one embodiment, the informational materialcan include information about production of the compound, molecularweight of the compound, concentration, date of expiration, batch orproduction site information, and so forth. In one embodiment, theinformational material relates to methods for administering thecompound. Additionally, the informational material of the kits is notlimited in its form. In many cases, the informational material, e.g.,instructions, is provided in printed matter, e.g., a printed text,drawing, and/or photograph, e.g., a label or printed sheet. However, theinformational material can also be provided in other formats, such asBraille, computer readable material, video recording, or audiorecording. In another embodiment, the informational material of the kitis contact information, e.g., a physical address, email address,website, or telephone number, where a user of the kit can obtainsubstantive information about a compound described herein and/or its usein the methods described herein. Of course, the informational materialcan also be provided in any combination of formats.

In one embodiment, the informational material can include instructionsto administer a compound(s) (e.g., small molecules of Formulas (I) or(II) (e.g., a IDE1 or IDE2 for Formula (I) or ILV for Formula (II)) asdescribed herein in a suitable manner to perform the methods describedherein, e.g., in a suitable dose, dosage form, or mode of administration(e.g., a dose, dosage form, or mode of administration described herein)(e.g., to a cell in vitro or a cell in vivo). In another embodiment, theinformational material can include instructions to administer acompound(s) described herein to a suitable subject, e.g., a human, e.g.,a human having or at risk for a disorder described herein or to a cellin vitro.

In addition to a compound(s) described herein, the composition of thekit can include other ingredients, such as a solvent or buffer, astabilizer, a preservative, a flavoring agent (e.g., a bitter antagonistor a sweetener), a fragrance or other cosmetic ingredient, and/or anadditional agent, e.g., for inducing pluripotent stem cells (e.g., invitro) or for treating a condition or disorder described herein.Alternatively, the other ingredients can be included in the kit, but indifferent compositions or containers than a compound described herein.In such embodiments, the kit can include instructions for admixing acompound(s) described herein and the other ingredients, or for using acompound(s) described herein together with the other ingredients, e.g.,instructions on combining the two agents prior to administration.

A compound of Formula (I), e.g. IDE1 or IDE2, or Formula (II), e.g. ILVas described herein can be provided in any form, e.g., liquid, dried orlyophilized form. It is preferred that a compound(s) described herein besubstantially pure and/or sterile. When a compound(s) d described hereinis provided in a liquid solution, the liquid solution preferably is anaqueous solution, with a sterile aqueous solution being preferred. Whena compound(s) described herein is provided as a dried form,reconstitution generally is by the addition of a suitable solvent. Thesolvent, e.g., sterile water or buffer, can optionally be provided inthe kit.

The kit can include one or more containers for the compositioncontaining at least one compound of Formula (I) and/or Formula (II) asdescribed herein. In some embodiments, the kit contains separatecontainers (e.g., two separate containers for the two agents), dividersor compartments for the composition(s) and informational material. Forexample, the composition can be contained in a bottle, vial, or syringe,and the informational material can be contained in a plastic sleeve orpacket. In other embodiments, the separate elements of the kit arecontained within a single, undivided container. For example, thecomposition is contained in a bottle, vial or syringe that has attachedthereto the informational material in the form of a label. In someembodiments, the kit includes a plurality (e.g., a pack) of individualcontainers, each containing one or more unit dosage forms (e.g., adosage form described herein) of a compound described herein. Forexample, the kit includes a plurality of syringes, ampules, foilpackets, or blister packs, each containing a single unit dose of acompound described herein. The containers of the kits can be air tight,waterproof (e.g., impermeable to changes in moisture or evaporation),and/or light-tight.

The kit optionally includes a device suitable for administration of thecomposition, e.g., a syringe, inhalant, pipette, forceps, measuredspoon, dropper (e.g., eye dropper), swab (e.g., a cotton swab or woodenswab), or any such delivery device. In a preferred embodiment, thedevice is a medical implant device, e.g., packaged for surgicalinsertion.

The kit can also include a component for the detection of a marker fordefinitive endoderm cell, e.g., for a marker described herein, e.g., areagent for the detection of positive definitive endoderm markers, e.g.Sox17 or Fox2A (HNF3β) or Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2,Ripk4, Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1, andRbm35. Or in some embodiments, the kit can also comprise reagents forthe detection of negative markers of definitive endoderm cells, e.g.Gata4, SPARC, APF, DAB, Zic, Pax6, Flk1 or CD31 for the purposes ofnegative selection of non-definitive endoderm cells or foridentification of cells which do not express these negative markers(e.g. definitive endoderm cells). The reagents can be, for example, anantibody against the marker or primers for a RT-PCR or PCR reaction,e.g., a semi-quantitative or quantitative RT-PCR or PCR reaction. Suchmarkers can be used to evaluate whether an iPS cell has been produced.If the detection reagent is an antibody, it can be supplied in drypreparation, e.g., lyophilized, or in a solution. The antibody or otherdetection reagent can be linked to a label, e.g., a radiological,fluorescent (e.g., GFP) or colorimetric label for use in detection. Ifthe detection reagent is a primer, it can be supplied in drypreparation, e.g., lyophilized, or in a solution.

It may be desirable to perform an analysis of the karyotype of thedefinitive endoderm cell or pdx1-positive pancreatic progenitor cell.Accordingly, the kit can include a component for karyotyping, e.g., aprobe, a dye, a substrate, an enzyme, an antibody or other usefulreagents for preparing a karyotype from a cell.

The kit can include definitive endoderm cell, e.g., an definitiveendoderm derived from the same type of pluripotent stem cell, forexample for the use as a positive cell type control. The kit can includePdx1-positive pancreatic progenitor, e.g., a Pdx1-positive pancreaticprogenitor derived from a definitive endoderm produced by contacting apluripotent stem cell with a compound of Formula (I), e.g. IDE1 or IDE1,for example for use as a positive cell type control.

The kit can also include informational materials, e.g., instructions,for use of two or more of the components included in the kit.

The informational material can be descriptive, instructional, marketingor other material that relates to the methods described herein and/orthe use of a compound(s) described herein for differentiating apluripotent stem cell according to the methods described herein. In oneembodiment, the informational material can include information aboutproduction of the compound, molecular weight of the compound,concentration, date of expiration, batch or production site information,and so forth. In one embodiment, the informational material relates tomethods for culturing a population of pluripotent stem cells in thepresence of a compound of Formula (I), and optionally, informationalmaterial relating to methods for culturing a population of definitiveendoderm cells in the presence of a compound of Formula (II).

Methods of Administering a Cell

In one embodiment, the cells described herein, e.g. a population ofdefinitive endoderm cells and/or a population of Pdx1-positivepancreatic progenitor cells are transplantable, e.g., a population ofdefinitive endoderm cells and/or a population of Pdx1-positivepancreatic progenitor cells can be administered to a subject. In someembodiment, the subject who is administered a population of definitiveendoderm cells and/or a population of Pdx1-positive pancreaticprogenitor cells is the same subject from whom a pluripotent stem cellused to differentiate into a definitive endoderm cell was obtained (e.g.for autologous cell therapy). In some embodiments, the subject is adifferent subject. In some embodiments, a subject suffering fromdiabetes such as type I diabetes, or is a normal subject. For example,the cells for transplantation (e.g. a composition comprising apopulation of definitive endoderm cells and/or a population ofPdx1-positive pancreatic progenitor cells) can be a form suitable fortransplantation, e.g., organ transplantation.

The method can further include administering the cells to a subject inneed thereof, e.g., a mammalian subject, e.g., a human subject. Thesource of the cells can be a mammal, preferably a human. The source orrecipient of the cells can also be a non-human subject, e.g., an animalmodel. The term “mammal” includes organisms, which include mice, rats,cows, sheep, pigs, rabbits, goats, horses, monkeys, dogs, cats, andpreferably humans. Likewise, transplantable cells can be obtained fromany of these organisms, including a non-human transgenic organism. Inone embodiment, the transplantable cells are genetically engineered,e.g., the cells include an exogenous gene or have been geneticallyengineered to inactivate or alter an endogenous gene.

A composition comprising a population of definitive endoderm cellsand/or a population of Pdx1-positive pancreatic progenitor cells can beadministered to a subject using an implantable device. Implantabledevices and related technology are known in the art and are useful asdelivery systems where a continuous, or timed-release delivery ofcompounds or compositions delineated herein is desired. Additionally,the implantable device delivery system is useful for targeting specificpoints of compound or composition delivery (e.g., localized sites,organs). Negrin et al., Biomaterials, 22(6):563 (2001). Timed-releasetechnology involving alternate delivery methods can also be used in thisinvention. For example, timed-release formulations based on polymertechnologies, sustained-release techniques and encapsulation techniques(e.g., polymeric, liposomal) can also be used for delivery of thecompounds and compositions delineated herein.

Pharmaceutical Compositions Comprising a Population of DefinitiveEndoderm Cells and/or a Population of Pdx1-Positive PancreaticProgenitor Cells

For administration to a subject, a cell populations produced by themethods as disclosed herein, e.g. a population of definitive endodermcells (produced by contacting a population of pluripotent stem cell witha compound of Formula (I) (e.g. IDE1 and/or IDE2)), or a population ofpdx1-positive progenitor cells (e.g. produced by contacting a populationof definitive endoderm cells with a compound of Formula (II) (e.g.Indolactam-V (ILV))) can be administered to a subject, for example in apharmaceutically acceptable compositions. These pharmaceuticallyacceptable compositions comprise a therapeutically-effective amount of apopulation of definitive endoderm cells or a population of Pdx1-positivepancreatic progenitor cells as described above, formulated together withone or more pharmaceutically acceptable carriers (additives) and/ordiluents.

As described in detail below, the pharmaceutical compositions of thepresent invention can be specially formulated for administration insolid or liquid form, including those adapted for the following: (1)oral administration, for example, drenches (aqueous or non-aqueoussolutions or suspensions), lozenges, dragees, capsules, pills, tablets(e.g., those targeted for buccal, sublingual, and systemic absorption),boluses, powders, granules, pastes for application to the tongue; (2)parenteral administration, for example, by subcutaneous, intramuscular,intravenous or epidural injection as, for example, a sterile solution orsuspension, or sustained-release formulation; (3) topical application,for example, as a cream, ointment, or a controlled-release patch orspray applied to the skin; (4) intravaginally or intrarectally, forexample, as a pessary, cream or foam; (5) sublingually; (6) ocularly;(7) transdermally; (8) transmucosally; or (9) nasally. Additionally,compounds can be implanted into a patient or injected using a drugdelivery system. See, for example, Urquhart, et al., Ann. Rev.Pharmacol. Toxicol. 24: 199-236 (1984); Lewis, ed. “Controlled Releaseof Pesticides and Pharmaceuticals” (Plenum Press, New York, 1981); U.S.Pat. Nos. 3,773,919; and 35 3,270,960.

As used here, the term “pharmaceutically acceptable” refers to thosecompounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

As used here, the term “pharmaceutically-acceptable carrier” means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, manufacturing aid (e.g.,lubricant, talc magnesium, calcium or zinc stearate, or steric acid), orsolvent encapsulating material, involved in carrying or transporting thesubject compound from one organ, or portion of the body, to anotherorgan, or portion of the body. Each carrier must be “acceptable” in thesense of being compatible with the other ingredients of the formulationand not injurious to the patient. Some examples of materials which canserve as pharmaceutically-acceptable carriers include: (1) sugars, suchas lactose, glucose and sucrose; (2) starches, such as corn starch andpotato starch; (3) cellulose, and its derivatives, such as sodiumcarboxymethyl cellulose, methylcellulose, ethyl cellulose,microcrystalline cellulose and cellulose acetate; (4) powderedtragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such asmagnesium stearate, sodium lauryl sulfate and talc; (8) excipients, suchas cocoa butter and suppository waxes; (9) oils, such as peanut oil,cottonseed oil, safflower oil, sesame oil, olive oil, corn oil andsoybean oil; (10) glycols, such as propylene glycol; (11) polyols, suchas glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12)esters, such as ethyl oleate and ethyl laurate; (13) agar; (14)buffering agents, such as magnesium hydroxide and aluminum hydroxide;(15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18)Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21)polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents,such as polypeptides and amino acids (23) serum component, such as serumalbumin, HDL and LDL; (22) C₂-C₁₂ alcohols, such as ethanol; and (23)other non-toxic compatible substances employed in pharmaceuticalformulations. Wetting agents, coloring agents, release agents, coatingagents, sweetening agents, flavoring agents, perfuming agents,preservative and antioxidants can also be present in the formulation.The terms such as “excipient”, “carrier”, “pharmaceutically acceptablecarrier” or the like are used interchangeably herein.

The phrase “therapeutically-effective amount” as used herein in respectto a population of cells means that amount of relevant cells in apopulation of cells, e.g., definitive endoderm cells and/orPdx1-positive pancreatic progenitor cells, or composition comprising adefinitive endoderm cells and/or Pdx1-positive pancreatic progenitorcells of the present invention which is effective for producing somedesired therapeutic effect in at least a sub-population of cells in ananimal at a reasonable benefit/risk ratio applicable to any medicaltreatment. For example, an amount of a population of definitive endodermcells and/or Pdx1-positive pancreatic progenitor cells administered to asubject that is sufficient to produce a statistically significant,measurable change in at least one symptom of Type 1, Type 1.5 or Type 2diabetes, such as glycosylated hemoglobin level, fasting blood glucoselevel, hypoinsulinemia, etc. Determination of a therapeuticallyeffective amount is well within the capability of those skilled in theart. Generally, a therapeutically effective amount can vary with thesubject's history, age, condition, sex, as well as the severity and typeof the medical condition in the subject, and administration of otherpharmaceutically active agents.

As used herein, the term “administer” refers to the placement of acomposition into a subject by a method or route which results in atleast partial localization of the composition at a desired site suchthat desired effect is produced. A compound or composition describedherein can be administered by any appropriate route known in the artincluding, but not limited to, oral or parenteral routes, includingintravenous, intramuscular, subcutaneous, transdermal, airway (aerosol),pulmonary, nasal, rectal, and topical (including buccal and sublingual)administration.

Exemplary modes of administration include, but are not limited to,injection, infusion, instillation, inhalation, or ingestion. “Injection”includes, without limitation, intravenous, intramuscular, intraarterial,intrathecal, intraventricular, intracapsular, intraorbital,intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous,subcuticular, intraarticular, sub capsular, subarachnoid, intraspinal,intracerebro spinal, and intrasternal injection and infusion. Inpreferred embodiments, the compositions are administered by intravenousinfusion or injection.

By “treatment”, “prevention” or “amelioration” of a disease or disorderis meant delaying or preventing the onset of such a disease or disorder,reversing, alleviating, ameliorating, inhibiting, slowing down orstopping the progression, aggravation or deterioration the progressionor severity of a condition associated with such a disease or disorder.In one embodiment, the symptoms of a disease or disorder are alleviatedby at least 5%, at least 10%, at least 20%, at least 30%, at least 40%,or at least 50%.

Treatment of Diabetes is determined by standard medical methods. A goalof Diabetes treatment is to bring sugar levels down to as close tonormal as is safely possible. Commonly set goals are 80-120 milligramsper deciliter (mg/dl) before meals and 100-140 mg/dl at bedtime. Aparticular physician may set different targets for the patent, dependingon other factors, such as how often the patient has low blood sugarreactions. Useful medical tests include tests on the patient's blood andurine to determine blood sugar level, tests for glycosylated hemoglobinlevel (HbA1c; a measure of average blood glucose levels over the past2-3 months, normal range being 4-6%), tests for cholesterol and fatlevels, and tests for urine protein level. Such tests are standard testsknown to those of skill in the art (see, for example, American DiabetesAssociation, 1998). A successful treatment program can also bedetermined by having fewer patients in the program with complicationsrelating to Diabetes, such as diseases of the eye, kidney disease, ornerve disease.

Delaying the onset of diabetes in a subject refers to delay of onset ofat least one symptom of diabetes, e.g., hyperglycemia, hypoinsulinemia,diabetic retinopathy, diabetic nephropathy, blindness, memory loss,renal failure, cardiovascular disease (including coronary arterydisease, peripheral artery disease, cerebrovascular disease,atherosclerosis, and hypertension), neuropathy, autonomic dysfunction,hyperglycemic hyperosmolar coma, or combinations thereof, for at least 1week, at least 2 weeks, at least 1 month, at least 2 months, at least 6months, at least 1 year, at least 2 years, at least 5 years, at least 10years, at least 20 years, at least 30 years, at least 40 years or more,and can include the entire lifespan of the subject.

In certain embodiments, the subject is a mammal, e.g., a primate, e.g.,a human. The terms, “patient” and “subject” are used interchangeablyherein. Preferably, the subject is a mammal. The mammal can be a human,non-human primate, mouse, rat, dog, cat, horse, or cow, but are notlimited to these examples. Mammals other than humans can beadvantageously used as subjects that represent animal models of Type 1diabetes, Type 2 Diabetes Mellitus, or pre-diabetic conditions. Inaddition, the methods described herein can be used to treat domesticatedanimals and/or pets. A subject can be male or female. A subject can beone who has been previously diagnosed with or identified as sufferingfrom or having Diabetes (e.g., Type 1 or Type 2), one or morecomplications related to Diabetes, or a pre-diabetic condition, andoptionally, but need not have already undergone treatment for theDiabetes, the one or more complications related to Diabetes, or thepre-diabetic condition. A subject can also be one who is not sufferingfrom Diabetes or a pre-diabetic condition. A subject can also be one whohas been diagnosed with or identified as suffering from Diabetes, one ormore complications related to Diabetes, or a pre-diabetic condition, butwho show improvements in known Diabetes risk factors as a result ofreceiving one or more treatments for Diabetes, one or more complicationsrelated to Diabetes, or the pre-diabetic condition. Alternatively, asubject can also be one who has not been previously diagnosed as havingDiabetes, one or more complications related to Diabetes, or apre-diabetic condition. For example, a subject can be one who exhibitsone or more risk factors for Diabetes, complications related toDiabetes, or a pre-diabetic condition, or a subject who does not exhibitDiabetes risk factors, or a subject who is asymptomatic for Diabetes,one or more Diabetes-related complications, or a pre-diabetic condition.A subject can also be one who is suffering from or at risk of developingDiabetes or a pre-diabetic condition. A subject can also be one who hasbeen diagnosed with or identified as having one or more complicationsrelated to Diabetes or a pre-diabetic condition as defined herein, oralternatively, a subject can be one who has not been previouslydiagnosed with or identified as having one or more complications relatedto Diabetes or a pre-diabetic condition.

As used herein, the phrase “subject in need of Pdx1-positive pancreaticprogenitor cells” refers to a subject who is diagnosed with oridentified as suffering from, having or at risk for developing diabetes(e.g., Type 1, Type 1.5 or Type 2), one or more complications related todiabetes, or a pre-diabetic condition.

A subject in need of Pdx1-positive pancreatic progenitor cells can beidentified using any method used for diagnosis of diabetes. For example,Type 1 diabetes can be diagnosed using a glycosylated hemoglobin (A1C)test, a random blood glucose test and/or a fasting blood glucose test.Parameters for diagnosis of diabetes are known in the art and availableto skilled artisan without much effort.

In some embodiments, the methods of the invention further compriseselecting a subject identified as being in need of additionalPdx1-positive pancreatic progenitor cells. A subject in need ofPdx1-positive pancreatic progenitor cells can be selected based on thesymptoms presented, such as symptoms of type 1, type 1.5 or type 2diabetes. Exemplary symptoms of diabetes include, but are not limitedto, excessive thirst (polydipsia), frequent urination (polyuria),extreme hunger (polyphagia), extreme fatigue, weight loss,hyperglycemia, low levels of insulin, high blood sugar (e.g., sugarlevels over 250 mg, over 300 mg), presence of ketones present in urine,fatigue, dry and/or itchy skin, blurred vision, slow healing cuts orsores, more infections than usual, numbness and tingling in feet,diabetic retinopathy, diabetic nephropathy, blindness, memory loss,renal failure, cardiovascular disease (including coronary arterydisease, peripheral artery disease, cerebrovascular disease,atherosclerosis, and hypertension), neuropathy, autonomic dysfunction,hyperglycemic hyperosmolar coma, and combinations thereof.

In some embodiments, a composition comprising a population of definitiveendoderm cells or pdx1-positive progenitors for administration to asubject can further comprise a pharmaceutically active agent, such asthose agents known in the art for treatment of diabetes and or forhaving anti-hyperglycemic activities, for example, inhibitors ofdipeptidyl peptidase 4 (DPP-4) (e.g., Alogliptin, Linagliptin,Saxagliptin, Sitagliptin, Vildagliptin, and Berberine), biguanides(e.g., Metformin, Buformin and Phenformin), peroxisomeproliferator-activated receptor (PPAR) modulators such asthiazolidinediones (TZDs) (e.g., Pioglitazone, Rivoglitazone,Rosiglitazone and Troglitazone), dual PPAR agonists (e.g., Aleglitazar,Muraglitazar and Tesaglitazar), sulfonylureas (e.g., Acetohexamide,Carbutamide, Chlorpropamide, Gliclazide, Tolbutamide, Tolazamide,Glibenclamide (Glyburide), Glipizide, Gliquidone, Glyclopyramide, andGlimepiride), meglitinides (“glinides”) (e.g., Nateglinide, Repaglinideand Mitiglinide), glucagon-like peptide-1 (GLP-1) and analogs (e.g.,Exendin-4, Exenatide, Liraglutide, Albiglutide), insulin and insulinanalogs (e.g., Insulin lispro, Insulin aspart, Insluin glulisine,Insulin glargine, Insulin detemir, Exubera and NPH insulin),alpha-glucosidase inhibitors (e.g., Acarbose, Miglitol and Voglibose),amylin analogs (e.g. Pramlintide), Sodium-dependent glucosecotransporter T2 (SGLT T2) inhibitors (e.g., Dapgliflozin, Remogliflozinand Sergliflozin) and others (e.g. Benfluorex and Tolrestat).

In type 1 diabetes, β-cells are undesirably destroyed by continuedautoimmune response. This autoimmune response may also destroydefinitive endoderm cells or pdx1-positive pancreatic progenitor cellsimplanted into a subject. Thus, this autoimmune response can beattenuated by use of compounds that inhibit or block such an autoimmuneresponse. In some embodiments, a composition comprising a population ofdefinitive endoderm cells or pdx1-positive progenitors foradministration to a subject can further comprise a pharmaceuticallyactive agent which is a immune response modulator. As used herein, theterm “immune response modulator” refers to compound (e.g., asmall-molecule, antibody, peptide, nucleic acid, or gene therapyreagent) that inhibits autoimmune response in a subject. Without wishingto be bound by theory, an immune response modulator inhibits theautoimmune response by inhibiting the activity, activation, orexpression of inflammatory cytokines (e.g., IL-12, IL-23 or IL-27), orSTAT-4. Exemplary immune response modulators include, bbut are notlimited to, members of the group consisting of Lisofylline (LSF) and theLSF analogs and derivatives described in U.S. Pat. No. 6,774,130,contents of which are herein incorporated by reference in theirentirety.

A composition comprising a definitive endoderm cell can be administratedto the subject in the same time, of different times as theadministration of a composition comprising pdx1-positive pancreaticprogenitors. When administrated at different times, the compositionscomprising a population of definitive endoderm cells and/orpdx1-positive progenitors for administration to a subject can beadministered within 5 minutes, 10 minutes, 20 minutes, 60 minutes, 2hours, 3 hours, 4, hours, 8 hours, 12 hours, 24 hours of administrationof the other. When a compositions comprising a population of definitiveendoderm cells and a composition comprising a population ofpdx1-positive progenitors are administered in different pharmaceuticalcompositions, routes of administration can be different. In someembodiments, a subject is administered a composition comprisingdefinitive endoderm cells. In other embodiments, a subject isadministered a composition comprising pdx1-positive pancreaticprogenitors. In another embodiment, a subject is administered acompositions comprising a population of definitive endoderm cells mixedwith a population of pdx1-positive progenitors. In another embodiment, asubject is administered a composition comprising a population ofdefinitive endoderm cells and a composition comprising a population ofpdxl-positive progenitors, where administration is substantially at thesame time, or subsequent to each other.

Toxicity and therapeutic efficacy of administration of a compositionscomprising a population of definitive endoderm cells and/orpdx1-positive progenitors can be determined by standard pharmaceuticalprocedures in cell cultures or experimental animals, e.g., fordetermining the LD50 (the dose lethal to 50% of the population) and theED50 (the dose therapeutically effective in 50% of the population).Compositions comprising a population of definitive endoderm cells and/orpdx1-positive progenitors that exhibit large therapeutic indices, arepreferred.

The amount of a composition comprising a population of definitiveendoderm cells and/or pdx1-positive progenitors can be tested usingseveral well-established animal models.

The non-obese diabetic (NOD) mouse carries a genetic defect that resultsin insulitis showing at several weeks of age (Yoshida et al., Rev.Immunogenet. 2:140, 2000). 60-90% of the females develop overt diabetesby 20-30 weeks. The immune-related pathology appears to be similar tothat in human Type I diabetes. Other models of Type I diabetes are micewith transgene and knockout mutations (Wong et al., Immunol. Rev.169:93, 1999). A rat model for spontaneous Type I diabetes was recentlyreported by Lenzen et al. (Diabetologia 44:1189, 2001). Hyperglycemiacan also be induced in mice (>500 mg glucose/dL) by way of a singleintraperitoneal injection of streptozotocin (Soria et al., Diabetes49:157, 2000), or by sequential low doses of streptozotocin (Ito et al.,Environ. Toxicol. Pharmacol. 9:71, 2001). To test the efficacy ofimplanted islet cells, the mice are monitored for return of glucose tonormal levels (<200 mg/dL).

Larger animals provide a good model for following the sequelae ofchronic hyperglycemia. Dogs can be rendered insulin-dependent byremoving the pancreas (J. Endocrinol. 158:49, 2001), or by feedinggalactose (Kador et al., Arch. Opthalmol. 113:352, 1995). There is alsoan inherited model for Type I diabetes in keeshond dogs (Am. J. Pathol.105:194, 1981). Early work with a dog model (Banting et al., Can. Med.Assoc. J. 22:141, 1922) resulted in a couple of Canadians making a longocean journey to Stockholm in February of 1925.

By way of illustration, a pilot study can be conducted by implanting apopulation of definitive endoderm cells or a population ofpdx1-pancreatic progenitors (or both) into the following animals: a)non-diabetic nude (T-cell deficient) mice; b) nude mice rendereddiabetic by streptozotocin treatment; and c) nude mice in the process ofregenerating islets following partial pancreatectomy. The number ofcells transplanted is equivalent to ˜1000-2000 normal human β-cellsimplanted under the kidney capsule, in the liver, or in the pancreas.For non-diabetic mice, the endpoints of can be assessment of graftsurvival (histological examination) and determination of insulinproduction by biochemical analysis, RIA, ELISA, andimmunohistochemistry. Streptozotocin treated and partiallypancreatectomized animals can also be evaluated for survival, metaboliccontrol (blood glucose) and weight gain.

In some embodiments, data obtained from the cell culture assays and inanimal studies can be used in formulating a range of dosage for use inhumans. The dosage of such compounds lies preferably within a range ofcirculating concentrations that include the ED50 with little or notoxicity. The dosage may vary within this range depending upon thedosage form employed and the route of administration utilized.

The therapeutically effective dose of a composition comprising apopulation of definitive endoderm cells and/or pdx1-positive progenitorscan also be estimated initially from cell culture assays. A dose may beformulated in animal models in vivo to achieve a secretion of insulin ata concentration which is appropriate in response to circulating glucosein the plasma. Alternatively, the effects of any particular dosage canbe monitored by a suitable bioassay.

With respect to duration and frequency of treatment, it is typical forskilled clinicians to monitor subjects in order to determine when thetreatment is providing therapeutic benefit, and to determine whether toincrease or decrease dosage, increase or decrease administrationfrequency, discontinue treatment, resume treatment or make otheralteration to treatment regimen. The dosing schedule can vary from oncea week to daily depending on a number of clinical factors, such as thesubject's sensitivity to the polypeptides. The desired dose can beadministered at one time or divided into subdoses, e.g., 2-4 subdosesand administered over a period of time, e.g., at appropriate intervalsthrough the day or other appropriate schedule. Such sub-doses can beadministered as unit dosage forms. In some embodiments, administrationis chronic, e.g., one or more doses daily over a period of weeks ormonths. Examples of dosing schedules are administration daily, twicedaily, three times daily or four or more times daily over a period of 1week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months,5 months, or 6 months or more.

In another aspect of the invention, the methods provide use of anisolated population of the definitive endoderm cells or pdx1-positivepancreatic progenitor cells as disclosed herein. In one embodiment ofthe invention, an isolated population of definitive endoderm cellsand/or pdx1-positive pancreatic progenitors as disclosed herein may beused for the production of a pharmaceutical composition, for the use intransplantation into subjects in need of treatment, e.g. a subject thathas, or is at risk of developing diabetes, for example but not limitedto subjects with congenital and acquired diabetes. In one embodiment, anisolated population of the definitive endoderm cells and/orpdx1-positive pancreatic progenitors may be genetically modified. Inanother aspect, the subject may have or be at risk of diabetes and/ormetabolic disorder. In some embodiments, an isolated population of thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein may be autologous and/or allogenic. In someembodiments, the subject is a mammal, and in other embodiments themammal is a human.

The use of an isolated population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein providesadvantages over existing methods because the definitive endoderm cellsand/or pdx1-positive pancreatic progenitors can be differentiated fromstem cells, e.g. iPS cells obtained or harvested from the subjectadministered an isolated population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors. This is highly advantageous as itprovides a renewable source of definitive endoderm cells and/orpdx1-positive pancreatic progenitors with can be differentiated in vitroor in vivo to insulin producing cells (e.g. pancreatic β-like cells orcells with pancreatic β-cell characteristics) by methods commonly knownby one of ordinary skill in the art, for transplantation into a subject,in particular a substantially pure population of definitive endodermcells and/or pdx1-positive pancreatic progenitors that do not have therisks and limitations of cells derived from other systems.

In another embodiment, an isolated population of definitive endodermcells and/or pdx1-positive pancreatic progenitors can be used as modelsfor studying properties for the differentiation into insulin-producingcells, e.g. to pancreatic β-cells or pancreatic β-like cells, orpathways of development of cells of endoderm origin into pancreaticβ-cells.

In some embodiments, the definitive endoderm cells and/or pdx1-positivepancreatic progenitors may be genetically engineered to comprise markersoperatively linked to promoters that are expressed when a marker isexpressed or secreted, for example, a marker can be operatively linkedto an insulin promoter, so that the marker is expressed when thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsare differentiated into insulin-producing cells which express andsecrete insulin. In some embodiments, a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors can be usedas a model for studying the differentiation pathway of cells whichdifferentiate into islet β-cells or pancreatic β-like cells.

In other embodiments, the definitive endoderm cells and/or pdx1-positivepancreatic progenitors can be used as models for studying the role ofislet β-cells in the pancreas and in the development of diabetes andmetabolic disorders. In some embodiments, the definitive endoderm cellsand/or pdx1-positive pancreatic progenitors can be from a normalsubject, or from a subject which carries a mutation and/or polymorphism(e.g. in the gene Pdx1 which leads to early-onset insulin-dependentdiabetes mellitus (NIDDM), as well as maturity onset diabetes of theyoung type 4 (MODY4), which can be use to identify small molecules andother therapeutic agents that can be used to treat subjects withdiabetes with a mutation or polymorphism in Pdx1. In some embodiments,the definitive endoderm cells and/or pdx1-positive pancreaticprogenitors may be genetically engineered to correct the polymorphism inthe Pdx1 gene prior to being administered to a subject in thetherapeutic treatment of a subject with diabetes. In some embodiments,the definitive endoderm cells and/or pdx1-positive pancreaticprogenitors may be genetically engineered to carry a mutation and/orpolymorphism.

In one embodiment of the invention relates to a method of treatingdiabetes or a metabolic disorder in a subject comprising administeringan effective amount of a composition comprising a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein to a subject with diabetes and/or a metabolic disorder.In a further embodiment, the invention provides a method for treatingdiabetes, comprising administering a composition comprising a populationof definitive endoderm cells and/or pdx1-positive pancreatic progenitorsas disclosed herein to a subject that has, or has increased risk ofdeveloping diabetes in an effective amount sufficient to produce insulinin response to increased blood glucose levels.

In one embodiment of the above methods, the subject is a human and apopulation of definitive endoderm cells and/or pdx1-positive pancreaticprogenitors as disclosed herein are human cells. In some embodiments,the invention contemplates that a population of definitive endodermcells and/or pdx1-positive pancreatic progenitors as disclosed hereinare administered directly to the pancreas of a subject, or isadministered systemically. In some embodiments, a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein can be administered to any suitable location in thesubject, for example in a capsule in the blood vessel or the liver orany suitable site where administered population of definitive endodermcells and/or pdx1-positive pancreatic progenitors can differentiate intoinsulin producing cells and can secrete insulin in response to increasedglucose levels in the subject.

The present invention is also directed to a method of treating a subjectwith diabetes or a metabolic disorder which occurs as a consequence ofgenetic defect, physical injury, environmental insult or conditioning,bad health, obesity and other diabetes risk factors commonly known by aperson of ordinary skill in the art. Efficacy of treatment of a subjectadministered a composition comprising a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors can bemonitored by clinically accepted criteria and tests, which include forexample, (i) Glycated hemoglobin (A1C) test, which indicates a subjectsaverage blood sugar level for the past two to three months, by measuringthe percentage of blood sugar attached to hemoglobin, theoxygen-carrying protein in red blood cells. The higher your blood sugarlevels, the more hemoglobin has sugar attached. An A1C level of 6.5percent or higher on two separate tests indicates the subject hasdiabetes. A test value of 6-6.5% suggest the subject has prediabetes.(ii) Random blood sugar test. A blood sample will be taken from thesubject at a random time, and a random blood sugar level of 200milligrams per deciliter (mg/dL)-11.1 millimoles per liter (mmol/L), orhigher indicated the subject has diabetes. (iii) Fasting blood sugartest. A blood sample is taken from the subject after an overnight fast.A fasting blood sugar level between 70 and 99 mg/dL (3.9 and 5.5 mmol/L)is normal. If the subjects fasting blood sugar levels is 126 mg/dL (7mmol/L) or higher on two separate tests, the subject has diabetes. Ablood sugar level from 100 to 125 mg/dL (5.6 to 6.9 mmol/L) indicatesthe subject has prediabetes. (iv) Oral glucose tolerance test. A bloodsample will be taken after the subject has fasted for at least eighthours or overnight and then ingested a sugary solution, and the bloodsugar level will be measured two hours later. A blood sugar level lessthan 140 mg/dL (7.8 mmol/L) is normal. A blood sugar level from 140 to199 mg/dL (7.8 to 11 mmol/L) is considered prediabetes. This issometimes referred to as impaired glucose tolerance (IGT). A blood sugarlevel of 200 mg/dL (11.1 mmol/L) or higher may indicate diabetes.

In some embodiments, the effects of administration of a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein to a subject in need thereof is associated withimproved exercise tolerance or other quality of life measures, anddecreased mortality. The effects of cellular therapy with definitiveendoderm cells and/or pdx1-positive pancreatic progenitors can beevident over the course of days to weeks after the procedure. However,beneficial effects may be observed as early as several hours after theprocedure, and may persist for several years.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein may be used fortissue reconstitution or regeneration in a human patient or othersubject in need of such treatment. In some embodiments compositions ofpopulations of definitive endoderm cells and/or pdx1-positive pancreaticprogenitors can be administered in a manner that permits them to graftor migrate to the intended tissue site and reconstitute or regeneratethe functionally deficient area. Special devices are available that areadapted for administering cells capable of reconstituting a populationof β-cells in the pancreas or at an alternative desired location.Accordingly, the definitive endoderm cells and/or pdx1-positivepancreatic progenitors may be administered to a recipient subject'spancreas by injection, or administered by intramuscular injection.

In some embodiments, compositions comprising a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors as disclosedherein have a variety of uses in clinical therapy, research,development, and commercial purposes. For therapeutic purposes, forexample, a population of definitive endoderm cells and/or pdx1-positivepancreatic progenitors as disclosed herein may be administered toenhance insulin production in response to increase in blood glucoselevel for any perceived need, such as an inborn error in metabolicfunction, the effect of a disease condition (e.g. diabetes), or theresult of significant trauma (i.e. damage to the pancreas or loss ordamage to islet β-cells). In some embodiments, a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein are administered to the subject not only help restorefunction to damaged or otherwise unhealthy tissues, but also facilitateremodeling of the damaged tissues.

To determine the suitability of cell compositions for therapeuticadministration, the definitive endoderm cells and/or pdx1-positivepancreatic progenitor cells can first be tested in a suitable animalmodel. At one level, cells are assessed for their ability to survive andmaintain their phenotype in vivo. Cell compositions comprisingdefinitive endoderm cells and/or pdx1-positive pancreatic progenitorscan be administered to immunodeficient animals (such as nude mice, oranimals rendered immunodeficient chemically or by irradiation). Tissuesare harvested after a period of regrowth, and assessed as to whether theadministered cells or progeny thereof are still present.

This can be performed by administering cells that express a detectablelabel (such as green fluorescent protein, or beta-galactosidase); thathave been prelabeled (for example, with BrdU or [3H] thymidine), or bysubsequent detection of a constitutive cell marker (for example, usinghuman-specific antibody). The presence and phenotype of the administeredpopulation of definitive endoderm cells and/or pdx1-positive pancreaticprogenitors can be assessed by immunohistochemistry or ELISA usinghuman-specific antibody, or by RT-PCR analysis using primers andhybridization conditions that cause amplification to be specific forhuman polynucleotides, according to published sequence data.

A number of animal models for testing diabetes are available for suchtesting, and are commonly known in the art, for example as disclosed inU.S. Pat. No. 6,187,991 which is incorporated herein by reference, aswell as rodent models; NOD (non-obese mouse), BB_DB mice, KDP rat andTCR mice, and other animal models of diabetes as described in Rees etal, Diabet Med. 2005 April; 22(4):359-70; Srinivasan K, et al., Indian JMed. Res. 2007 March; 125(3):451-7; Chatzigeorgiou A, et al., In Vivo.2009 March-April; 23(2):245-58, which are incorporated herein byreference.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein may beadministered in any physiologically acceptable excipient, where thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsmay find an appropriate site for regeneration and differentiation. Insome embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein can beintroduced by injection, catheter, or the like. In some embodiments, apopulation of definitive endoderm cells and/or pdx1-positive pancreaticprogenitors as disclosed herein can be frozen at liquid nitrogentemperatures and stored for long periods of time, being capable of useon thawing. If frozen, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors will usually be stored in a 10%DMSO, 50% FCS, 40% RPMI 1640 medium. Once thawed, the cells may beexpanded by use of growth factors and/or feeder cells associated withculturing 13 definitive endoderm cells and/or pdx1-positive pancreaticprogenitors as disclosed herein.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein can be suppliedin the form of a pharmaceutical composition, comprising an isotonicexcipient prepared under sufficiently sterile conditions for humanadministration. For general principles in medicinal formulation, thereader is referred to Cell Therapy: Stem Cell Transplantation, GeneTherapy, and Cellular Immunotherapy, by G. Morstyn & W. Sheridan eds,Cambridge University Press, 1996; and Hematopoietic Stem Cell Therapy,E. D. Ball, J. Lister & P. Law, Churchill Livingstone, 2000. Choice ofthe cellular excipient and any accompanying elements of the compositioncomprising a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein will be adaptedin accordance with the route and device used for administration. In someembodiments, a composition comprising a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors can alsocomprise or be accompanied with one or more other ingredients thatfacilitate the engraftment or functional mobilization of the definitiveendoderm cells and/or pdx1-positive pancreatic progenitors. Suitableingredients include matrix proteins that support or promote adhesion ofthe definitive endoderm cells and/or pdx1-positive pancreaticprogenitors, or complementary cell types, especially endothelial cells.In another embodiment, the composition may comprise resorbable orbiodegradable matrix scaffolds.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors as disclosed herein may begenetically altered in order to introduce genes useful in differentiatedprogeny, e.g. genes useful in insulin producing cells such as pancreaticβ-cells, e.g. repair of a genetic defect in an individual, selectablemarker, etc., or genes useful in selection against non-insulin producingcells differentiated from a definitive endoderm cell and/orpdx1-positive pancreatic progenitor cell or for the selective suicide ofimplanted definitive endoderm cells and/or pdx1-positive pancreaticprogenitors. In some embodiments, a population of definitive endodermcells and/or pdx1-positive pancreatic progenitors can also begenetically modified to enhance survival, control proliferation, and thelike. In some embodiments, a population of definitive endoderm cellsand/or pdx1-positive pancreatic progenitors as disclosed herein can begenetically altering by transfection or transduction with a suitablevector, homologous recombination, or other appropriate technique, sothat they express a gene of interest. In one embodiment, a definitiveendoderm cell and/or pdx1-positive pancreatic progenitor is transfectedwith genes encoding a telomerase catalytic component (TERT), typicallyunder a heterologous promoter that increases telomerase expressionbeyond what occurs under the endogenous promoter, (see InternationalPatent Application WO 98/14592, which is incorporated herein byreference). In other embodiments, a selectable marker is introduced, toprovide for greater purity of the population of definitive endodermcells and/or pdx1-positive pancreatic progenitors. In some embodiments,a population of definitive endoderm cells and/or pdx1-positivepancreatic progenitors may be genetically altered using vectorcontaining supernatants over a 8-16 h period, and then exchanged intogrowth medium for 1-2 days. Genetically altered definitive endodermcells and/or pdx1-positive pancreatic progenitors can be selected usinga drug selection agent such as puromycin, G418, or blasticidin, and thenrecultured.

Gene therapy can be used to either modify a cell to replace a geneproduct, to facilitate regeneration of tissue, to treat disease, or toimprove survival of the cells following implantation into a subject(i.e. prevent rejection).

In an alternative embodiment, a population of definitive endoderm cellsand/or pdx1-positive pancreatic progenitors as disclosed herein can alsobe genetically altered in order to enhance their ability to be involvedin tissue regeneration, or to deliver a therapeutic gene to a site ofadministration. A vector is designed using the known encoding sequencefor the desired gene, operatively linked to a promoter that is eitherpan-specific or specifically active in the differentiated cell type. Ofparticular interest are cells that are genetically altered to expressone or more growth factors of various types, such as somatostatin,glucagon, and other factors.

Many vectors useful for transferring exogenous genes into targetdefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein are available. The vectors may be episomal, e.g.plasmids, virus derived vectors such as cytomegalovirus, adenovirus,etc., or may be integrated into the target cell genome, throughhomologous recombination or random integration, e.g. retrovirus derivedvectors such MMLV, HIV-1, ALV, etc. In some embodiments, combinations ofretroviruses and an appropriate packaging cell line may also find use,where the capsid proteins will be functional for infecting thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitors asdisclosed herein. Usually, definitive endoderm cells and/orpdx1-positive pancreatic progenitors and virus will be incubated for atleast about 24 hours in the culture medium. In some embodiments, thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsare then allowed to grow in the culture medium for short intervals insome applications, e.g. 24-73 hours, or for at least two weeks, and maybe allowed to grow for five weeks or more, before analysis. Commonlyused retroviral vectors are “defective”, i.e. unable to produce viralproteins required for productive infection. Replication of the vectorrequires growth in the packaging cell line.

The host cell specificity of the retrovirus is determined by theenvelope protein, env (p120). The envelope protein is provided by thepackaging cell line. Envelope proteins are of at least three types,ecotropic, amphotropic and xenotropic. Retroviruses packaged withecotropic envelope protein, e.g. MMLV, are capable of infecting mostmurine and rat cell types. Ecotropic packaging cell lines include BOSC23(Pear et al. (1993) P.N.A.S. 90:8392-8396). Retroviruses bearingamphotropic envelope protein, e.g. 4070A (Danos et al, supra.), arecapable of infecting most mammalian cell types, including human, dog andmouse. Amphotropic packaging cell lines include PAl2 (Miller et al.(1985) Mol. Cell. Biol. 5:431-437); PA317 (Miller et al. (1986) Mol.Cell. Biol. 6:2895-2902) GRIP (Danos et al. (1988) PNAS 85:6460-6464).Retroviruses packaged with xenotropic envelope protein, e.g. AKR env,are capable of infecting most mammalian cell types, except murine cells.In some embodiments, the vectors may include genes that must later beremoved, e.g. using a recombinase system such as Cre/Lox, or the cellsthat express them destroyed, e.g. by including genes that allowselective toxicity such as herpesvirus TK, Bc1-Xs, etc.

Suitable inducible promoters are activated in a desired target celltype, either the transfected cell, or progeny thereof. Bytranscriptional activation, it is intended that transcription will beincreased above basal levels in the target cell by at least about 100fold, more usually by at least about 1000 fold. Various promoters areknown that are induced in different cell types.

In one aspect of the present invention, a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors as disclosedherein are suitable for administering systemically or to a targetanatomical site. A population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors can be grafted into or nearby asubject's pancreas, for example, or may be administered systemically,such as, but not limited to, intra-arterial or intravenousadministration. In alternative embodiments, a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors of thepresent invention can be administered in various ways as would beappropriate to implant in the pancreatic or secretory system, includingbut not limited to parenteral, including intravenous and intraarterialadministration, intrathecal administration, intraventricularadministration, intraparenchymal, intracranial, intracisternal,intrastriatal, and intranigral administration. Optionally, a populationof definitive endoderm cells and/or pdx1-positive pancreatic progenitorsare administered in conjunction with an immunosuppressive agent.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors can be administered and dosed inaccordance with good medical practice, taking into account the clinicalcondition of the individual patient, the site and method ofadministration, scheduling of administration, patient age, sex, bodyweight and other factors known to medical practitioners. Thepharmaceutically “effective amount” for purposes herein is thusdetermined by such considerations as are known in the art. The amountmust be effective to achieve improvement, including but not limited toimproved survival rate or more rapid recovery, or improvement orelimination of symptoms and other indicators as are selected asappropriate measures by those skilled in the art. A population ofdefinitive endoderm cells and/or pdxl-positive pancreatic progenitorscan be administered to a subject the following locations: clinic,clinical office, emergency department, hospital ward, intensive careunit, operating room, catheterization suites, and radiologic suites.

In other embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors is stored for laterimplantation/infusion. A population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors may be divided into more than onealiquot or unit such that part of a population of definitive endodermcells and/or pdx1-positive pancreatic progenitors is retained for laterapplication while part is applied immediately to the subject. Moderateto long-term storage of all or part of the cells in a cell bank is alsowithin the scope of this invention, as disclosed in U.S. PatentApplication Serial No. 20030054331 and Patent Application No.WO03024215, and is incorporated by reference in their entireties. At theend of processing, the concentrated cells may be loaded into a deliverydevice, such as a syringe, for placement into the recipient by any meansknown to one of ordinary skill in the art.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors can be applied alone or incombination with other cells, tissue, tissue fragments, growth factorssuch as VEGF and other known angiogenic or arteriogenic growth factors,biologically active or inert compounds, resorbable plastic scaffolds, orother additive intended to enhance the delivery, efficacy, tolerability,or function of the population. In some embodiments, a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsmay also be modified by insertion of DNA or by placement in cell culturein such a way as to change, enhance, or supplement the function of thecells for derivation of a structural or therapeutic purpose. Forexample, gene transfer techniques for stem cells are known by persons ofordinary skill in the art, as disclosed in (Morizono et al., 2003; Moscaet al., 2000), and may include viral transfection techniques, and morespecifically, adeno-associated virus gene transfer techniques, asdisclosed in (Walther and Stein, 2000) and (Athanasopoulos et al.,2000). Non-viral based techniques may also be performed as disclosed in(Murarnatsu et al., 1998).

In another aspect, in some embodiments, a population of definitiveendoderm cells and/or pdx1-positive pancreatic progenitors could becombined with a gene encoding pro-angiogenic growth factor(s). Genesencoding anti-apoptotic factors or agents could also be applied.Addition of the gene (or combination of genes) could be by anytechnology known in the art including but not limited to adenoviraltransduction, “gene guns,” liposome-mediated transduction, andretrovirus or lentivirus-mediated transduction, plasmid adeno-associatedvirus. Cells could be implanted along with a carrier material bearinggene delivery vehicle capable of releasing and/or presenting genes tothe cells over time such that transduction can continue or be initiated.Particularly when the cells and/or tissue containing the cells areadministered to a patient other than the patient from whom the cellsand/or tissue were obtained, one or more immunosuppressive agents may beadministered to the patient receiving the cells and/or tissue to reduce,and preferably prevent, rejection of the transplant. As used herein, theterm “immunosuppressive drug or agent” is intended to includepharmaceutical agents which inhibit or interfere with normal immunefunction. Examples of immunosuppressive agents suitable with the methodsdisclosed herein include agents that inhibit T-cell/B-cell costimulationpathways, such as agents that interfere with the coupling of T-cells andB-cells via the CTLA4 and B7 pathways, as disclosed in U.S. Patent Pub.No 2002/0182211, which is incorporated herein by reference. In oneembodiment, a immunosuppressive agent is cyclosporine A. Other examplesinclude myophenylate mofetil, rapamicin, and anti-thymocyte globulin. Inone embodiment, the immunosuppressive drug is administered with at leastone other therapeutic agent. The immunosuppressive drug is administeredin a formulation which is compatible with the route of administrationand is administered to a subject at a dosage sufficient to achieve thedesired therapeutic effect. In another embodiment, the immunosuppressivedrug is administered transiently for a sufficient time to inducetolerance to the cardiovascular stem cells of the invention.

Pharmaceutical compositions comprising effective amounts of a populationof definitive endoderm cells and/or pdx1-positive pancreatic progenitorsare also contemplated by the present invention. These compositionscomprise an effective number of definitive endoderm cells and/orpdx1-positive pancreatic progenitors, optionally, in combination with apharmaceutically acceptable carrier, additive or excipient. In certainaspects of the present invention, a population of definitive endodermcells and/or pdx1-positive pancreatic progenitors are administered tothe subject in need of a transplant in sterile saline. In other aspectsof the present invention, a population of definitive endoderm cellsand/or pdx1-positive pancreatic progenitors are administered in HanksBalanced Salt Solution (HBSS) or Isolyte S, pH 7.4. Other approaches mayalso be used, including the use of serum free cellular media. In oneembodiment, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors are administered in plasma or fetalbovine serum, and DMSO. Systemic administration of a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitorscells to the subject may be preferred in certain indications, whereasdirect administration at the site of or in proximity to the diseasedand/or damaged tissue may be preferred in other indications.

In some embodiments, a population of definitive endoderm cells and/orpdx1-positive pancreatic progenitors can optionally be packaged in asuitable container with written instructions for a desired purpose, suchas the reconstitution or thawing (if frozen) of a population ofdefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsprior to administration to a subject.

In one embodiment, an isolated population of definitive endoderm cellsand/or pdx1-positive pancreatic progenitors as disclosed herein areadministered with a differentiation agent. In one embodiment, thedefinitive endoderm cells and/or pdx1-positive pancreatic progenitorsare combined with the differentiation agent to administration into thesubject. In another embodiment, the cells are administered separately tothe subject from the differentiation agent. Optionally, if the cells areadministered separately from the differentiation agent, there is atemporal separation in the administration of the cells and thedifferentiation agent. The temporal separation may range from about lessthan a minute in time, to about hours or days in time. The determinationof the optimal timing and order of administration is readily androutinely determined by one of ordinary skill in the art.

Diagnosis of Diabetes

Type 1 diabetes is an autoimmune disease that results in destruction ofinsulin-producing beta cells of the pancreas. Lack of insulin causes anincrease of fasting blood glucose (around 70-120 mg/dL in nondiabeticpeople) that begins to appear in the urine above the renal threshold(about 190-200 mg/dl in most people). The World Health Organizationdefines the diagnostic value of fasting plasma glucose concentration to7.0 mmol/l (126 mg/dl) and above for Diabetes Mellitus (whole blood 6.1mmol/l or 110 mg/dl), or 2-hour glucose level of 11.1 mmol/L or higher(200 mg/dL or higher).

Type 1 diabetes can be diagnosed using a variety of diagnostic teststhat include, but are not limited to, the following: (1) glycatedhemoglobin (A1C) test, (2) random blood glucose test and/or (3) fastingblood glucose test.

The Glycated hemoglobin (A1C) test is a blood test that reflects theaverage blood glucose level of a subject over the preceding two to threemonths. The test measures the percentage of blood glucose attached tohemoglobin, which correlates with blood glucose levels (e.g., the higherthe blood glucose levels, the more hemoglobin is glycosylated). An A1Clevel of 6.5 percent or higher on two separate tests is indicative ofdiabetes. A result between 6 and 6.5 percent is considered prediabetic,which indicates a high risk of developing diabetes.

The Random Blood Glucose Test comprises obtaining a blood sample at arandom time point from a subject suspected of having diabetes. Bloodglucose values can be expressed in milligrams per deciliter (mg/dL) ormillimoles per liter (mmol/L). A random blood glucose level of 200 mg/dL(11.1 mmol/L) or higher indicates the subject likely has diabetes,especially when coupled with any of the signs and symptoms of diabetes,such as frequent urination and extreme thirst.

For the fasting blood glucose test, a blood sample is obtained after anovernight fast. A fasting blood glucose level less than 100 mg/dL (5.6mmol/L) is considered normal. A fasting blood glucose level from 100 to125 mg/dL (5.6 to 6.9 mmol/L) is considered prediabetic, while a levelof 126 mg/dL (7 mmol/L) or higher on two separate tests is indicative ofdiabetes.

Type 1 diabetes can also be distinguished from type 2 diabetes using aC-peptide assay, which is a measure of endogenous insulin production.The presence of anti-islet antibodies (to Glutamic Acid Decarboxylase,Insulinoma Associated Peptide-2 or insulin), or lack of insulinresistance, determined by a glucose tolerance test, is also indicativeof type 1, as many type 2 diabetics continue to produce insulininternally, and all have some degree of insulin resistance.

Testing for GAD 65 antibodies has been proposed as an improved test fordifferentiating between type 1 and type 2 diabetes as it appears thatthe immune system is involved in Type 1 diabetes etiology.

In some embodiments, the present invention provides compositions for theuse of populations of definitive endoderm cells or populations ofpdx1-positive pancreatic progenitor cells produced by the methods asdisclosed herein or their differentiated progeny to restore isletfunction in a subject in need of such therapy. Any condition relating toinadequate production of a pancreatic endocrine (insulin, glucagon, orsomatostatin), or the inability to properly regulate secretion may beconsidered for treatment with cells (e.g. populations of definitiveendoderm cells or populations of pdx1-positive pancreatic progenitorcells) prepared according to this invention, as appropriate. Of especialinterest is the treatment of Type I (insulin-dependent) diabetesmellitus.

Subjects in need thereof can be selected for treatment based onconfirmed long-term dependence on administration of exogenous insulin,and acceptable risk profile. The subject receives approximately 10,000definitive endoderm cells or pdx1-positive pancreatic progenitor cellsequivalents per kg body weight. If the cells are not autologouse, inorder to overcome an allotype mismatch, the subject can be treatedbefore surgery with an immunosuppressive agent such as FK506 andrapamycin (orally) and daclizumab (intravenously). A compositioncomprising a populations of definitive endoderm cells and/or populationof pdx1-positive pancreatic progenitor cells can be infused through acatheter in the portal vein. The subject can then be subjected toabdominal ultrasound and blood tests to determine liver function. Dailyinsulin requirement is tracked, and the subject is given a secondtransplant if required. Follow-up monitoring includes frequent bloodtests for drug levels, immune function, general health status, andwhether the patient remains insulin independent.

General approaches to the management of the diabetic patient areprovided in standard textbooks, such as the Textbook of InternalMedicine, 3rd Edition, by W. N. Kelley ed., Lippincott-Raven, 1997; andin specialized references such as Diabetes Mellitus: A Fundamental andClinical Text 2nd Edition, by D. Leroith ed., Lippincott Williams &Wilkins 2000; Diabetes (Atlas of Clinical Endocrinology Vol. 2) by C. R.Kahn et al. eds., Blackwell Science 1999; and Medical Management of Type1 Diabetes 3rd Edition, McGraw Hill 1998. Use of islet cells for thetreatment of Type I diabetes is discussed at length in CellularInter-Relationships in the Pancreas: Implications for IsletTransplantation, by L. Rosenberg et al., Chapman & Hall 1999; and FetalIslet Transplantation, by C. M. Peterson et al. eds., Kluwer 1995.

As always, the ultimate responsibility for subject selection, the modeof administration, and dosage of a population of definitive endodermcells or a population of pdx1-positive pancreatic progenitor cells isthe responsibility of the managing clinician. For purposes of commercialdistribution, populations of definitive endoderm cells or populations ofpdx1-positive pancreatic progenitor cells as disclosed herein aretypically supplied in the form of a pharmaceutical composition,comprising an isotonic excipient prepared under sufficiently sterileconditions for human administration. This invention also includes setsof population of definitive endoderm cells or populations ofpdx1-positive pancreatic progenitor cells that exist at any time duringtheir manufacture, distribution, or use. The sets of populations ofdefinitive endoderm cells or populations of pdx1-positive pancreaticprogenitor cells comprise any combination of two or more cellpopulations described in this disclosure, exemplified but not limited tothe differentiation of definitive endoderm cells to become pdx1-positivepancreatic progenitor cells, and their subsequent differentiation e.g.into insulin-producing cells such as pancreatic β-cells or pancreaticβ-like cells as the term is defined herein. In some embodiments, thecell compositions comprising populations of definitive endoderm cells orpopulations of pdx1-positive pancreatic progenitor cells can beadministered (e.g. implanted into a subject) in combination with othercell types e.g. other differentiated cell types, sometimes sharing thesame genome. Each cell type in the set may be packaged together, or inseparate containers in the same facility, or at different locations,under control of the same entity or different entities sharing abusiness relationship.

For general principles in medicinal formulation of cell compositions,the reader is referred to Cell Therapy: Stem Cell Transplantation, GeneTherapy, and Cellular Immunotherapy, by G. Morstyn & W. Sheridan eds,Cambridge University Press, 1996. The composition is optionally packagedin a suitable container with written instructions for a desired purpose,such as the treatment of diabetes.

In some embodiments, compositions comprising populations of definitiveendoderm cells or populations of pdx1-positive pancreatic progenitorcells can also be used as the functional component in a mechanicaldevice designed to produce one or more of the endocrine polypeptides ofpancreatic islet cells. In its simplest form, the device contains apopulation of definitive endoderm cells or populations of pdx1-positivepancreatic progenitor cells behind a semipermeable membrane thatprevents passage of the cell population, retaining them in the device,but permits passage of insulin, glucagon, or somatostatin secreted bythe cell population. This includes populations of definitive endodermcells or populations of pdx1-positive pancreatic progenitor cells thatare microencapsulated, typically in the form of cell clusters to permitthe cell interaction that inhibits dedifferentiation. For example, U.S.Pat. No. 4,391,909 describe islet cells encapsulated in a spheroidsemipermeable membrane made up of polysaccharide polymers>3,000 mol. wt.that are cross-linked so that it is permeable to proteins the size ofinsulin, but impermeable to molecules over 100,000 mol. wt. U.S. Pat.No. 6,023,009 describes islet cells encapsulated in a semipermeablemembrane made of agarose and agaropectin. Microcapsules of this natureare adapted for administration into the body cavity of a diabeticpatient, and are thought to have certain advantages in reducinghistocompatibility problems or susceptibility to bacteria.

More elaborate devices are also contemplated for use to comprise apopulation of definitive endoderm cells or a population of pdx1-positivepancreatic progenitor cells, either for implantation into diabeticpatients, or for extracorporeal therapy. U.S. Pat. No. 4,378,016describes an artificial endocrine gland containing an extracorporealsegment, a subcutaneous segment, and a replaceable envelope containingthe hormone-producing cells. U.S. Pat. No. 5,674,289 describes abioartificial pancreas having an islet chamber, separated by asemipermeable membrane to one or more vascularizing chambers open tosurrounding tissue. Useful devices typically have a chamber adapted tocontain the islet cells, and a chamber separated from the islet cells bya semipermeable membrane which collects the secreted proteins from theislet cells, and which may also permit signaling back to the isletcells, for example, of the circulating glucose level.

Methods of Identifying Compounds that Increase the Production ofEndoderm

Described herein is a method of identifying a compound that increasesthe production of endoderm. In certain examples, a high content and/orhigh throughput screening method is provided. The method includesexposing a stem cell (e.g., an ES cell) to at least one compound (e.g.,a library compound or a compound described herein) and determining ifthe compound increases the production of endoderm, e.g., definitiveendoderm from the stem cells. A cell can be identified as an endoderm(e.g., a definitive endoderm) using one or more of the markers describedherein. In some examples, the stem cells may be differentiated prior toexposure to the library. In other examples, two or more compounds may beused, either individually or together, in the screening assay. Inadditional examples, the stem cells may be placed in a multi-well plate,and a library of compounds may be screened by placing the variousmembers of the library in different wells of the multi-well plate. Suchscreening of libraries can rapidly identify compounds that are capableof endoderm, e.g., definitive endoderm, from the stem cells.

In one aspect, the invention features a method of producing anendodermal cell, e.g., a definitive endoderm cell, the method comprisingexposing a stem cell, e.g., an embryonic stem (ES) cell to an effectiveamount of at least one compound described herein, e.g., a compound offormula (I) e.g., IDE1 and/or IDE2, or an HDAC inhibitor(s), todifferentiate the stem cell into the endodermal cell, e.g., thedefinitive endodermal cell. In some embodiments, the stem cell is from amammal. In some embodiments, the stem cell is from mouse or human. Insome embodiments, the stem cell is an embryonic stem cell (e.g., amammalian embryonic stem cell such as a mouse or human embryonic stemcell). In some embodiments, a plurality of stem cells are differentiatedinto a plurality of endodermal cells, e.g., definitive endodermal cells.

In some embodiments, the method further comprises isolating a populationof the endodermal cells, e.g., definitive endodermal cells (e.g.,wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 50%, 75% or greaterof the subject cell type). In some embodiments, the compound is an HDACinhibitor. In some embodiments, the compound is a compound of formula(I)

wherein

-   each R¹ and R² is independently H, alkyl, or arylalkyl;-   each R³ and R⁴ is independently H or optionally substituted cycyl,    heterocycyll, aryl, or heteroaryl; or R³ and R⁴ taken together with    the carbon to which they are attached, form a ring; and-   L is C₂₋₁₀ alkylenyl, C₂₋₁₀heteroalkylenyl, C₂₋₁₀ alkenylenyl, or    C₂₋₁₀ alkynylenyl.

In some embodiments, the compound is IDE1 or IDE2. In some embodiments,the stem cell is exposed to the compound, e.g., an HDAC inhibitor(s) ora compound of formula (I) e.g., IDE1 and/or IDE2, for about 1, 2, 4, 6,8, 10, 12, 14, 16, or more days. In some embodiments, the stem cell isexposed to the compound, e.g., an HDAC inhibitor(s) or a compound offormula (I), e.g., IDE1 and/or IDE2, for 6 days. In some embodiments,the stem cell is exposed to the compound, e.g., an HDAC inhibitor(s) ora compound of formula (I), e.g., IDE1 and/or IDE2, at a concentration ofabout 25 nM, 50 nM, 100 nM, 150 nM, 200 nM, 250 nM, 400 nM, 500 nM, 600nM, 700 nM, 800 nM, 1 μM, 21 μM, 3 μM, 4 μM, 5 μM or 10 μM. In someembodiments, the stem cell is exposed to the compound, e.g., an HDACinhibitor(s) or a compound of formula (I), e.g., IDE1 and/or IDE2, at aconcentration of about 250 nM, 400 nM, 500 nM, 600 nM, 700 nM, or 800nM. In some embodiments, greater than about 20%, 30%, 40%, 50%, 60%,70%, 80%, or 90% of the stems cells are differentiated into theendodermal cells, e.g., definitive endodermal cells.

In some embodiments, the method further comprises exposing the stemcells to at least one additional agent. In some embodiments, theadditional agent is Nodal, Activin A or Wnt3a. In some embodiments, theendodermal cell, e.g., the definitive endodermal cell is a Sox17+ cell.In some embodiments, the expression of a marker selected from the groupconsisting of: Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4,Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Sox17, andRbm35a is upregulated to by a statistically significant amount in theendodermal cell, e.g., the definitive endodermal cell relative to thestem cell. In some embodiments, the expression of a marker selected fromthe group consisting of: Gata4, SPARC, AFP and Dab2 is not upregulatedto by a statistically significant amount in the endodermal cell, e.g.,the definitive endodermal cell relative to the stem cell. In someembodiments, the expression of a marker selected from the groupconsisting of: Zic1, Pax6, Flk1 and CD31 is not upregulated to by astatistically significant amount in the endodermal cell, e.g., thedefinitive endodermal cell relative to the stem cell. In someembodiments, the phosphorylation of Smad2 is upregulated to by astatistically significant amount in the endodermal cell, e.g., thedefinitive endodermal cell relative to the stem cell. In someembodiments, at least one of the components in the TGFβ signalingpathway is activated by a statistically significant level in theendodermal cell, e.g., the definitive endodermal cell relative to thestem cell. In some embodiments, the endodermal cell, e.g., thedefinitive endodermal cell has the capacity to integrate into thedeveloping gut tube in vivo. In some embodiments, the endodermal cell,e.g., the definitive endodermal cell can differentiate into a cellhaving the characteristic morphology of a gut cell and expressingmarkers of gut tube, e.g., FoxA2 and/or Claudin6, in vivo.

In some embodiments, the method further comprises differentiating theendodermal cell, e.g., the definitive endodermal cell into a cell of asecond cell type. In some embodiments, the cell of the second cell typeis a cell of gastrointestinal tract; a cell of respiratory tract; or acell of endocrine gland, e.g., a liver cell, a pancreatic cell, or apancreatic cell precursor. In some embodiments, the cell of the secondcell type is a pancreatic cell or a pancreatic cell precursor, e.g. aPdx1-positive pancreatic progenitor. In some embodiments, the pancreaticcell or pancreatic precursor cell, e.g. a Pdx1-positive pancreaticprogenitor is a Pdx1+ cell or an HNF6+ cell. In some embodiments, themethod further comprises exposing the endoderm cell, e.g., thedefinitive endoderm cell to FGF10 and a Hedgehog signaling inhibitor,e.g., KAAD-cyclopamine. In some embodiments, the method furthercomprises exposing the endoderm cell, e.g., the definitive endoderm cellto a posteriorizing factor, e.g., retinoic acid. In some embodiments,the method further comprises exposing the endoderm cell, e.g., thedefinitive endoderm cell to an effective amount of Indolactam V. In someembodiments, a plurality of endodermal cells, e.g., definitiveendodermal cells, are differentiated into a plurality of cells of asecond cell type, e.g. a cell of endoderm origin such as, but notlimited to a pdx1-positive pancreatic progenitor. In some embodiments,the method further comprises isolating a population of the cells of thesecond cell type (e.g. a cell of endoderm origin, for example, apdx1-positive pancreatic progenitors), wherein at least 5%, 10%, 15%,20%, 25%, 30%, 35%, 50%, 75% or greater of the subject cell type (e.g.the second cell type or pdx1-positive pancreatic progenitors) areisolated.

In some embodiments, the method further comprises implanting the cellsof definitive endoderm produced by the methods as disclosed herein, orimplanting the second cell type e.g. a cell of endoderm origin, forexample, a pdx1-positive pancreatic progenitors into a subject (e.g., asubject having diabetes, e.g., type I, type II or Type 1.5 diabetes). Insome embodiments, the stem cell is from a subject. In some embodiments,the stem cell is from a donor different than the subject, e.g., arelative of the subject.

In one aspect, the invention features an endoderm cell, e.g. adefinative endoderm cell made by a method described herein. In anotheraspect, the invention features a composition comprising an endoderm cellmade by a method described herein. In yet another aspect, the inventionfeatures a second cell type (e.g. a pdx1-positive pancreatic progenitor)made by a method described herein. In one aspect, the invention featuresa composition comprising a second cell type (e.g. a pdx1-positivepancreatic progenitor) made by a method described herein.

In another aspect, the invention features a kit comprising: a stemcells, e.g., an ES cell; at least one compound described herein, e.g.,an HDAC inhibitor(s) or a compound of formula (I), e.g., IDE1 and/orIDE2; and instructions for using the stem cells and the at least onecompound to produce an endodermal cell, e.g., a definitive endodermcell. In some embodiments, the kit further comprises: a component forthe detection of a marker for an endodermal cell, e.g., for a markerdescribed herein, e.g., a reagent for the detection of Nodal, Tmprss2,Tmem30b, St14, Spink3, Sh3gl2, Ripk4, Rab15, Npnt, Clic6, Cldn8,Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Sox17, and Rbm35a, e.g., an antibodyagainst the marker; and an endodermal cell, e.g., a definitiveendodermal cell, e.g., for use as a control. In some embodiments, thekit further comprises: a component to differentiate an endodermal cell,e.g., a definitive endodermal cell to a cell of a second cell type,e.g., a pancreatic cell or pancreatic cell precursors; and instructionsfor using the endodermal cell (e.g., the definitive endodermal cell)described herein and the component to produce the cell of a second type,e.g., pancreatic cell or pancreatic cell precursors. In someembodiments, the kit further comprises: a component for the detection ofa marker for the cell of the second cell type, e.g., for a markerdescribed herein, e.g., a reagent for the detection of Pdx1, e.g., anantibody against the marker; and a cell or the second cell type, e.g., apancreatic cell or a pancreatic cell precursor, e.g., for use as acontrol.

In one aspect, the invention features a method of facilitatingdifferentiation of a stem cell, e.g., an ES cell, to an endodermal cell,e.g., definitive endoderm comprising providing a stem cell, andproviding at least one compound described herein, e.g., an HDACinhibitor(s) or a compound of formula (I), e.g., IDE1 and/or IDE2, todifferentiate the stem cell to provide the endodermal cell, e.g.,definitive endodermal cell, upon exposure of the stem cell to the atleast one compound. In some embodiments, the stem cell is from a mammal.In some embodiments, the stem cell is from mouse or human. In someembodiments, the stem cell is an embryonic stem cell (e.g., a mammalianembryonic stem cell such as a mouse or human embryonic stem cell).

In some embodiments, a plurality of stem cells are differentiated into aplurality of endoderm cells, e.g., definitive endodermal cells. In someembodiments, the compound is IDE1 or IDE2. In some embodiments, the stemcell is exposed to the compound, e.g., an HDAC inhibitor(s) or acompound of formula (I) e.g., IDE1 and/or IDE2, for about 1, 2, 4, 6, 8,10, 12, 14, 16, or more days. In some embodiments, the stem cell isexposed to the compound, e.g., an HDAC inhibitor(s) or a compound offormula (I), e.g., IDE1 and/or IDE2, for 6 days. In some embodiments,the stem cell is exposed to the compound, e.g., an HDAC inhibitor(s) ora compound of formula (I), e.g., IDE1 and/or IDE2, at a concentration ofabout 25 nM, 50 nM, 100 nM, 150 nM, 200 nM, 250 nM, 400 nM, 500 nM, 600nM, 700 nM, 800 nM, 1 μM, 2 μM, 3 μM, 4 μM, 5 μM or 10 μM. In someembodiments, the stem cell is exposed to the compound, e.g., an HDACinhibitor(s) or a compound of formula (I), e.g., IDE1 and/or IDE2, at aconcentration of about 250 nM, 400 nM, 500 nM, 600 nM, 700 nM, or 800nM. In some embodiments, greater than about 20%, 30%, 40%, 50%, 60%,70%, 80%, or 90% of the stems cells are differentiated into theendodermal cells, e.g., definitive endodermal cells. In someembodiments, the method further comprises exposing the stem cells to atleast one additional agent. In some embodiments, the additional agent isNodal, Activin A or Wnt3a.

The present invention may be as defined in any one of the followingnumbered paragraphs.

-   1. A method of producing a definitive endoderm cell from a    pluripotent stem cell comprising contacting a population of    pluripotent stem cells with at least one compound of Formula (I) to    induce the differentiation of at least one pluripotent stem cell    into a definitive endoderm cell, wherein the definitive endoderm    cell expresses Sox17, or HNF3B (FoxA2), or Sox17 and HNF3B (FoxA2)    and wherein the compound of formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   -   2. The method of paragraph 1, wherein the pluripotent stem cell        is an embryonic stem (ES) cell.    -   3. The method of paragraphs 1 or 2, wherein the pluripotent stem        cell is an induced pluripotent stem (iPS) cell.    -   4. The method of any of paragraphs 1 to 3, wherein the stem cell        is from a mammal.    -   5. The method of any of paragraphs 1 to 4, wherein the stem cell        is a human stem cell.    -   6. The method of any of paragraphs 1 to 5, wherein the method        further comprising isolating a population of definitive endoderm        cells, wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 50%,        75% or greater of the total cells in the isolated population are        definitive endoderm cells.    -   7. The method of any of paragraphs 1 to 6, wherein the compound        of formula (I) is IDE1 having the structure:

-   8. The method of any of paragraphs 1 to 6, wherein the compound of    formula (I) is IDE2 having the structure:

-   9. The method of any of paragraphs 1 to 8, wherein the compound of    Formula (I) is an HDAC inhibitor.-   10. The method of any of paragraphs 1 to 9, wherein the pluripotent    stem cell is contacted with the compound of Formula (I) for at least    1 day.-   11. The method of any of paragraphs 1 to 10, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) for at least 6    days.-   12. The method of any of paragraphs 1 to 11, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) at a    concentration of between 25 nM-10 μM.-   13. The method of any of paragraphs 1 to 12, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE1    at a concentration of between 50 nM-5 μM.-   14. The method of any of paragraphs 1 to 13, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE1    at a concentration of at least 50 nM.-   15. The method of any of paragraphs 1 to 14, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE1    at a concentration of at least 100 nM.-   16. The method of any of paragraphs 1 to 15, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE2    at a concentration of between 50 nM-5 μM.-   17. The method of any of paragraphs 1 to 16, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE2    at a concentration of at least 100 nM.-   18. The method of any of paragraphs 1 to 17, wherein the pluripotent    stem cell is contacted with a compound of Formula (I) which is IDE2    at a concentration of at least 200 nM.-   19. The method of any of paragraphs 1 to 18, wherein at least 20% of    the pluripotent stem cells in the population of pluripotent stem    cells are induced to differentiate a definitive endoderm cell.-   20. The method of any of paragraphs 1 to 19, wherein at least 40% of    the pluripotent stem cells in the population of pluripotent stem    cells are induced to differentiate a definitive endoderm cell.-   21. The method of any of paragraphs 1 to 20, wherein at between    80-90% of the pluripotent stem cells in the population of    pluripotent stem cells are induced to differentiate a definitive    endoderm cell.-   22. The method of any of paragraphs 1 to 21, the method further    comprising exposing the stem cells to at least one additional agent.-   23. The method of any of paragraphs 1 to 22, wherein the additional    agent is selected from the group consisting of: Nodal, Activin A or    Wnt3a.-   24. The method of any of paragraphs 1 to 23, wherein the definitive    endoderm cell expresses at least one marker selected from the group    consisting of: Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2, Ripk4,    Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1, Sox17,    and Rbm35a, wherein the expression of at least one marker is    upregulated to by a statistically significant amount in the    definitive endoderm cell relative to the pluripotent stem cell from    which it was derived.-   25. The method of any of paragraphs 1 to 24, wherein the definitive    endoderm cell does not express by a statistically significant amount    at least one marker selected the group consisting of: Gata4, SPARC,    AFP and Dab2 relative to the pluripotent stem cell from which it was    derived.-   26. The method of any of paragraphs 1 to 25, wherein the definitive    endoderm cell does not express by a statistically significant amount    at least one marker selected the group consisting of: Zic1, Pax6,    Flk1 and CD31 relative to the pluripotent stem cell from which it    was derived.-   27. The method of any of paragraphs 1 to 26, wherein the definitive    endoderm cell has a higher level of phosphorylation of Smad2 by a    statistically significant amount relative to the pluripotent stem    cell from which it was derived.-   28. The method of any of paragraphs 1 to 27, wherein the definitive    endoderm cell has the capacity to form gut tube in vivo.-   29. The method of any of paragraphs 1 to 28, wherein the definitive    endoderm cell can differentiate into a cell with morphology    characteristic of a gut cell, and wherein a cell with morphology    characteristic of a gut cell expresses FoxA2 and/or Claudin6.-   30. The method of any of paragraphs 1 to 29, further comprising    differentiating the definitive endoderm cell into a cell of endoderm    origin.-   31. The method of any of paragraphs 1 to 29, further comprising    differentiating the definitive endoderm cell into a Pdx1-positive    pancreatic progenitor cell, wherein the Pdx1-positive pancreatic    progenitor cell expresses Pdx1.-   32. The method of paragraph 31, wherein a Pdx1-positive pancreatic    progenitor cell also expresses HNF6.    33. The method of paragraphs 31 or 32, comprising contacting a    population of definitive endoderm cells with at least one compound    of Formula (II) to induce the differentiation of at least one    definitive endoderm cell into a Pdx1-positive pancreatic progenitor    cell, wherein the compound of formula (II) is:

R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or cyclyl,each of which can be optionally substituted;

R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl, alkynyl,alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can beoptionally substituted; and

R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl, alkenyl,alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or cyclyl, eachof which can be optionally substituted, or R²⁴ and R²⁵ together with thecarbons to which they are attached form an optionally substitutedcyclyl.

-   34. The method of any of paragraphs 31 to 33, wherein the compound    of Formula (II) is    (2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one    ((−)-indolactam V).-   35. The method of any of paragraphs 31 to 34, further comprising    isolating the population of Pdx1-positive pancreatic progenitor    cells.-   36. The method of any of paragraphs 31 to 35, further comprising    differentiating the population of Pdx1-positive pancreatic    progenitor cells into a population of insulin producing cells.-   37. The method of any of paragraphs 31 to 37, further comprising    differentiating the population of Pdx1-positive pancreatic    progenitor cells into a population of cells having at least one    characteristic of endogenous pancreatic β-cells.-   38. The method of any of paragraphs 31 to 37, wherein a cell with at    least one characteristic of an endogenous pancreatic β-cell is    secretion of insulin in response to glucose.-   39. The method of any of paragraphs 31 to 38, further comprising    implanting a population of Pdx1-positive pancreatic progenitor cells    or their differentiated progeny of insulin producing cells or cells    having at least one characteristic of endogenous pancreatic β-cells    into a subject in need thereof.-   40. The method of any of paragraphs 31 to 39, wherein the subject in    need thereof has diabetes, or is at risk of developing diabetes.-   41. The method of any of paragraphs 3 to 40, wherein the induced    pluripotent stem (iPS) cell is from a subject with diabetes or at    risk of developing diabetes.-   42. An isolated population of definitive endoderm cells obtained    from a population of pluripotent stem cells by a process comprising    contacting the population of pluripotent stem cells with at least    one compound of Formula (I), wherein the compound of Formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   43. An isolated population of definitive endoderm cells obtained    from a population of pluripotent stem cells by a process comprising    contacting the population of pluripotent stem cells with at least    one compound of IDE1 or IDE2, wherein the compound of IDE1 having    the structure:

and the compound of IDE2 having the structure:

-   44. An isolated population of Pdx1-positive pancreatic progenitors    obtained from a population of pluripotent stem cells by a process    comprising: (i) contacting the population of pluripotent stem cells    with at least one compound of Formula (I) to induce the    differentiation of at least one pluripotent stem cell into    definitive endoderm cell, and; (ii) contacting at least one    definitive endoderm cell with at least one compound of Formula (II)    to induce the differentiation of at least one definitive endoderm    cell into a Pdx1-positive progenitor cell.-   45. The isolated population of Pdx1-positive pancreatic progenitors    of paragraph 44, wherein the compound of Formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   46. The isolated population of Pdx1-positive pancreatic progenitors    of paragraph 44 or 45, wherein the compound of Formula (I) is    selected from IDE1 or IDE2, wherein the compound of IDE1 having the    structure:

and the compound of IDE2 having the structure:

-   47. The isolated population of Pdx1-positive pancreatic progenitors    of any of paragraphs 44 to 46, wherein the compound of Formula (II)    is:

R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or cyclyl,each of which can be optionally substituted;

R²² and R²³ independently H, halogen, OH, alkyl, alkenyl, alkynyl,alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can beoptionally substituted; and

R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl, alkenyl,alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or cyclyl, eachof which can be optionally substituted, or R²⁴ and R²⁵ together with thecarbons to which they are attached form an optionally substitutedcyclyl.

-   48. The isolated population of Pdx1-positive pancreatic progenitors    of any of paragraphs 44 to 47, wherein the compound of Formula (II)    is    (2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one    ((−)-indolactam V).-   49. A composition comprising a population of definitive endoderm    cells produced according to the methods of any of paragraphs 1-30.-   50. A composition comprising a population of Pdx1-positive    pancreatic progenitor cells produced according to the methods of any    of paragraphs 1 to 41 or 44 to 49.-   51. A method for the treatment of a subject with diabetes, the    method comprising administering to a subject a composition    comprising an isolated population of Pdx1-positive pancreatic    progenitor cells of any of paragraphs 44 to 49, or progeny thereof.-   52. The method of paragraph 51, wherein the Pdx1-positive pancreatic    progenitor cells are produced from a population of pluripotent stem    cells obtained from the same subject as the Pdx1-positive pancreatic    progenitor cells are administered to.-   53. The method of paragraph 51 or 52, wherein the Pdx1-positive    pancreatic progenitor cells are produced from an population of iPS    cell, wherein the iPS cell is derived from a cell obtained from the    same subject as the Pdx1-positive pancreatic progenitor cells are    administered to.-   54. The method of any of paragraphs 51 to 53, wherein the subject    has, or has an increased risk of developing diabetes.-   55. The method of any of paragraphs 51 to 54, wherein the diabetes    is selected from the group of Type I diabetes, Type II diabetes,    Type 1.5 diabetes and pre-diabetes.-   56. The method of any of paragraphs 51 to 55, wherein the subject    has, or has increased risk of developing a metabolic disorder.-   57. Use of an isolated population of definitive endoderm cells    produced by the methods according to paragraphs 1 to 30 or 42 to 43    for differentiating into Pdx1-positive pancreatic progenitors.-   58. Use of an isolated population of definitive endoderm cells    produced by the methods according to paragraphs 1 to 30 or 42 to 43    for differentiating into a cell of endoderm origin.-   59. The use of paragraph 58, wherein the cell of endoderm origin is    a cell selected from the group consisting of: a liver cell, a    epithelial cell, a pancreatic cell, a pancreatic endoderm (PE) cell,    a tymus cell, an intestine cell, a stomach cell, a thyroid cell and    a lung cell.    60. Use of an isolated population of Pdx1-positive progenitors    produced by the methods according to paragraphs 1 to 41 or 44 to 48    for administering to a subject in need thereof.-   61. The use of paragraph 60, wherein the subject has, or has an    increased risk of developing diabetes.-   62. The use of paragraphs 60 or 61, wherein the diabetes is selected    from the group of Type I diabetes, Type II diabetes, Type 1.5 and    pre-diabetes.-   63. The use of any of paragraphs 60 to 62, wherein the subject has,    or has increased risk of developing a metabolic disorder.-   64. A kit comprising at least one compound of Formula (I), wherein    the compound of Formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   65. The kit of paragraph 64, wherein the compound of Formula (I) is    selected from IDE1 or IDE2, wherein the compound of IDE1 having the    structure:

and the compound of IDE2 having the structure:

-   66. The kit of paragraph 64 or 65, further comprising at least one    compound of Formula (II), wherein the compound of Formula (II) is:

R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or cyclyl,each of which can be optionally substituted;

R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl, alkynyl,alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can beoptionally substituted; and

R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl, alkenyl,alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or cyclyl, eachof which can be optionally substituted, or R²⁴ and R²⁵ together with thecarbons to which they are attached form an optionally substitutedcyclyl.

-   67. The kit of any of paragraphs 64 to 66, wherein the compound of    Formula (II) is    (2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one    ((−)-indolactam V).-   68. The kit of any of paragraphs 64 to 67, wherein the kit further    comprises an isolated population of pluripotent stem cells.-   69. The kit of any of paragraphs 64 to 68, wherein the isolated    population of pluripotent stem cells is a control population of    pluripotent stem cells.-   70. The kit of any of paragraphs 64 to 69, further comprising a    control cell population selected from the group of; an endoderm cell    population, a definitive endoderm cell population, a pluripotent    cell population, a Pdx1-positive pancreatic progenitor cell    population.-   71. The kit of any of paragraphs 64 to 70, further comprising at    least one agent for the detection of a marker for a definitive    endoderm cell, wherein the marker can be selected from any of the    group consisting of; Nodal, Tmprss2, Tmem30b, St14, Spink3, Sh3gl2,    Ripk4, Rab15, Npnt, Clic6, Cldn8, Cacna1b, Bnip1, Anxa4, Emb, FoxA1,    Sox17, and Rbm35a.-   72. The kit of any of paragraphs 64 to 71, further comprising at    least one agent for the detection of a marker for a Pdx1-positive    pancreatic progenitor, wherein the marker can be selected from any    of the group consisting of; Pdx1 and HNF6.-   73. A reaction admixture comprising a definitive endoderm cell and    at least one compound of Formula (I), wherein the compound of    Formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   74. The reaction admixture of paragraph 73, wherein the compound of    Formula (I) is selected from IDE1 or IDE2, wherein the compound of    IDE1 having the structure:

and the compound of IDE2 having the structure:

-   75. The reaction admixture of paragraphs 73 or 74, wherein the    definitive endoderm cell is a human definitive endoderm cell.-   76. A reaction admixture comprising a Pdx1-positive progenitor cell    and at least one compound of Formula (II), wherein the compound of    Formula (II) is:

R²¹ is H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, cyclyl, or cyclyl,each of which can be optionally substituted;

R²² and R²³ are independently H, halogen, OH, alkyl, alkenyl, alkynyl,alkoxy, aryl, heteroaryl, cyclyl, or cyclyl, each of which can beoptionally substituted; and

R²⁴ and R²⁵ are each independently H, halogen, OH, SH, alkyl, alkenyl,alkynyl, alkoxy, thioalkoxy, aryl, heteroaryl, cyclyl, or cyclyl, eachof which can be optionally substituted, or R²⁴ and R²⁵ together with thecarbons to which they are attached form an optionally substitutedcyclyl.

-   77. The reaction admixture of paragraph 76, wherein the compound of    Formula (II) is    (2S,5S)-1,2,4,5,6,8-Hexahydro-5-(hydroxymethyl)-1-methyl-2-(1-methylethyl)-3H-pyrrolo[4,3,2-gh]-1,4-benzodiazonin-3-one    ((−)-indolactam V).-   78. The reaction admixture of paragraph 76 or 77, wherein the    Pdx1-positive progenitor cell is a human Pdx1-positive progenitor    cell.-   79. The reaction admixture of any of paragraphs 76 to 78, wherein    the Pdx1-positive progenitor cell has been differentiated from a    definitive endoderm cell, wherein the definitive endoderm cell has    differentiated from a pluripotent stem cell by contacting the    pluripotent stem cell with a compound of Formula (I).-   80. The reaction admixture of any of paragraph 76 to 79, wherein the    admixture further comprises at least one compound of Formula (I),    wherein the compound of Formula (I) is:

wherein:

R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O);

R³ and R⁴ are independently H, halogen, alkyl, alkenyl, alkynyl, alkoxy,aryl, heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted, or R³ and R⁴ together with the carbon to which they areattached from an optionally substituted cyclyl of heterocycyl; and

L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl, or C₂-C₁₀ alkynylenyl, eachof which can be optionally substituted and/or can be interrupted in thebackbone with one or more of O, N, S, S(O), and C(O).

-   81. The reaction admixture of any of paragraphs 76 to 80, wherein    the compound of Formula (I) is selected from IDE1 or IDE2, wherein    the compound of IDE1 having the structure:

and the compound of IDE2 having the structure:

-   82. The reaction admixture of any of paragraphs 76 to 81, wherein    the definitive endoderm cell is a human definitive endoderm cell.

In some embodiments, the methods described herein have one or more ofthe following advantages over other methods of making endoderm known inthe art: the ability to produce endoderm, e.g., reduced cost ofproducing endoderm; easier and/or simplified production of endoderm,e.g., definitive endoderm, using a small molecule such as a compounddescribed herein (for example, as opposed to a protein or otherbiological molecule); or increased efficiency in generating endoderm,e.g., definitive endoderm from stem cells. In some embodiments, a methoddescribed herein results in the production of Sox17+ endoderm, e.g.,Sox17+ definitive endoderm by exposure to a small molecule compound suchas a compound described herein.

In some embodiments, the methods described herein have one or more ofthe following advantages over other methods of the generation ofpancreatic lineage cells by differentiation of endoderm (e.g.,definitive endoderm) relative to other methods known in the art.Exemplary advantages include the ability to produce pancreatic cells andpancreatic precursor cells at low cost, easier and simplified productionof pancreatic cells and pancreatic precursor cells, and increasedefficiency in generating pancreatic cells and pancreatic precursorcells. In some embodiments, the methods described herein result in theproduction of Pdx1+ pancreatic cells and pancreatic precursor cells fromendoderm (e.g., definitive endoderm) produced by the methods describedherein.

In some examples, statistically significant means there is statisticalevidence that there is a difference; it does not mean the difference isnecessarily large, important, or significant in the common meaning ofthe word. The significance level of a test is a traditional frequentiststatistical hypothesis testing concept. It can be defined as theprobability of making a decision to reject the null hypothesis when thenull hypothesis is actually true (a decision known as a Type I error, or“false positive determination”). The decision is often made using thep-value: if the p-value is less than the significance level, then thenull hypothesis is rejected. The significance level of a test can alsomean a probability such that the probability of making a decision toreject the null hypothesis when the null hypothesis is actually true isno more than the stated probability. This allows for those applicationswhere the probability of deciding to reject may be much smaller than thesignificance level for some sets of assumptions encompassed within thenull hypothesis.

EXAMPLES

Many modifications and variations of this invention can be made withoutdeparting from its spirit and scope, as will be apparent to thoseskilled in the art. The specific embodiments described herein areoffered by way of example only, and the invention is to be limited onlyin terms of the appended claims, along with the full scope ofequivalents to which such claims are entitled.

Experimental Procedures

Mouse ES cells culture and differentiation. Mouse ES cells wereroutinely cultured on irradiated CF-1 MEF feeder cells in DMEM (Gibco)media supplemented with 15% Fetal Bovine Serum (HyClone FBS,Invitrogen), 2 mM L-glutamine (L-Glu, Gibco), 1.1 mM 2-mercaptoethanol(Gibco), 1 mM nonessential amino acids (Gibco),1×penicillin/streptomycin (P/S, Gibco) and 5×10⁵ units LIF (Chemicon).Cells were passaged at the ratio of 1:6-1:12 every 2-3 days using 0.25%trypsin. To generate the starting population, mouse ES cells wascultured on MEF feeder cells until they reached 80-90% confluence. Priorto differentiation, ES cells were passaged onto gelatin coated platesfor 30 min to remove MEFs. MEF depleted ES cells were seeded at 2500cells per cm² on gelatinized plates. After overnight culture, cells wereexposed to 25 ng/ml Wnt3a (R&D Systems)+50 ng/ml recombinant Activin A(R&D Systems) or 500 ng/ml Nodal (R&D Systems) in DMEM (Gibco)supplemented with 1×L-Glu and 0.2% FBS (Gibco) for 1 day, then Activin Aor Nodal in the same media and cultured for 4-6 days to induce endodermdifferentiation. For the chemical inductions, compounds IDE1 and IDE2(provided by Stuart L. Schreiber) were added at 5 μM concentration inthe differentiation media. For pancreatic progenitors induction, thecells were transferred to 50 ng/ml FGF10 (R&D Systems), 0.75 μMKAAD-cyclopamine (Calbiochem) and 21.1M RA (Sigma) or Indolactam V 330nM (Axxora) in DMEM supplemented with 1×L-Glu, 1×PS, 1×B27 (Invitrogen)for 4 days. SB431542 was purchased from Sigma. All stock compounds weremade with either DMSO or PBS

High throughput screen. To carry out the screen, mouse Sox17/dsRed EScells (passage 16-20) were trypsinized, MEF depleted, and plated ongelatin-coated 384-well plates at density 800 cells/well using BiotekμFill. After overnight incubation in regular mouse ES media, the mediawas changed to low serum containing differentiating media (2% FBS) andcompounds were added by pin transfer at final concentration 5 μM, in avolume 50 μl per well containing 1% DMSO (v/v). After an additional 6days of culture, cells were washed twice with PBS, trypsinized for 3min, suspended in FACS buffer (PBS, 5% FBS) and dsRed expression wasdetected by high throughput FACS analysis (Aria, Becton Dickinson).

Chemical libraries. The compound libraries used for this study included:the MicroSource library consisting of 2,000 bioactive compounds andknown drugs, 1,000 synthetic compounds biased for HDAC inhibition(obtained from Stuart L. Schreiber laboratory) and a selection ofhand-picked known modulators of stem cell fate (20 compounds), smallmolecule microarray consisting of approximately 400 compounds, includingbioactives, natural products, and 400 compounds that are knownmodulators of development or signaling pathways (both prepared by StuartL. Schreiber laboratory).

HUESC culture and differentiation. Human embryonic stem cell lines werecultured essentially as described {Cowan, 2004 #6}. Briefly, HUES4,HUES8 and HUES9 cells are routinely cultured on irradiated CF-1 MEFfeeder cells in KnockOut DMEM (Gibco) supplemented with 10% KnockOutSerum Replacement (Gibco), 10% human plasma (Invitrogen), 2 mML-glutamine (L-Glu, Gibco), 1.1 mM 2-mercaptoethanol (Gibco), 1 mMnonessential amino acids (Gibco), 1×penicillin/streptomycin (PS, Gibco)and 10 ng/ml bFGF (Invitrogen). Cells are split at the ratio of1:10-1:12 every 4-5 days by using 1 mg/ml collagenase type IV. To induceendoderm formation, HUES cells was cultured on MEF feeder cells till80-90% confluent, then treated with 100 ng/ml Activin A in advanced RPMI(Gibco) supplemented with 1xL-Glu and 0.2% FBS (Gibco), or withcombination of 25 ng/ml Wnt3a (R&D systems)+100 ng/ml Activin A (R&Dsystems) or were exposed to compounds in the same media. At days 4 and 6of culture cells were analysed for endodermal marker expression, Sox17.

Immunocytochemistry. Cells were fixed in 4% paraformaldehyde (Sigma) inPBS for 20 min at 4° C. followed by a wash with PBS. Cells were blockedwith 10% donkey serum (Jackson Immunoresearch) in PBS/0.1% Triton X andincubated with primary antibodies overnight at 4° C. Secondaryantibodies were incubated for 1 h at room temperature. The followingantibodies and dilutions were used: goat anti-SOX17, (1:500 R&Dsystems); rabbit anti-PDX1 (1:200,Chemicon), rabbit anti-FoxA2 (1:500;Upstate), rabbit anti-Dab2 (1:200, Santa Cruz), rabbit anti-SPARC(1:200, Santa Cruz), mouse anti-AFP (1:100, Sigma), anti-Gata6 (1:50,Santa Cruz Biotech), goat anti-HNF6 (1:200, Santa Cruz Biotech), rabbitanti-RFP/DsRed (1:300, MBL), rabbit anti-GFP (1:200, Molecular Probes).Secondary antibodies were: rhodamine Red-X-conjugated donkey anti-goatantibody, 1:200 (JIRL), Alexa-488-conjugated goat anti-mouse andAlexa-594-conjugated goat anti-rabbit antibodies (1:300, MolecularProbes). Nuclei were visualized by Hoechst 33342 (1:1000, MolecularProbes). Images were taken using an Olympus IX70 Microscope. Forquantification images were analyzed for the frequency of SOX17+, FoxA2+or Pdx1+ cells using Metamorph image analysis software (MolecularDevices) and at least 6 images per well were collected. Data wereconfirmed in four independent experiments.

Flow cytometry. Cells were dissociated using 0.25% trypsin for 3 minfollowed by quenching of trypsin and further dissociation in PBS with 5%FBS. Suspension was filtered through nylon and cells were analysed andsorted out by MoFlo (Dako Cytomation, Ft. Collins, Colo.).

Quantification of endoderm formation. Endoderm formation was monitoredby Sox17 expression by either flow cytometry detection of Sox17/DsRed orimmunofluorescence using anti-Sox17 antibodies. Cells labeled byantibody staining were quantified using Metamorph software ad percentageof total cell number (based on Hoechst 33342 nuclei staining). Allconditions were tested in either tri- or quadruplicates.

Global gene expression analysis. Sox17/DsRed+ cells were sorted out byFACS from mouse cell cultures treated either with growth factors orcompounds. Total RNA was isolated using Qiashredder and RNAeasy Mini Kit(both from Qiagen). Biotinylated cRNA was prepared from ≧100 ng ofisolated RNA using Illumina TotalPrep RNA Amplification Kit (Ambion) andhybridized to the Illumina mouse genome Bead Chips (MouseRef8). Allsamples were prepared as three biological replicates. Data were acquiredwith Illumina Beadstation 500 and were evaluated using BeadStudio DataAnalysis Software (Illumina)

Western Blot analysis. Cells were lysed in 1×RIPA lysis buffer in thepresence of protease inhibitor mixture (Roche)/1% phosphatase inhibitormixture (Roche). Proteins were separated by 10% Tris-Glycine SDS/PAGE(Bio-rad) under denaturing conditions and transferred to anitrocellulose membrane. After blocking with 5% skim milk in PBS/0.1%Triton X, the membrane was incubated with primary antibodies againstphospho-Smad2 (1:1000, Cell Signaling) overnight at 4° C. The membranewas then washed, incubated with anti-mouse/rabbit peroxidase-conjugatedaffinity-purified secondary antibody (1:1000, Cell Signaling) at roomtemperature for 1 h, and developed by SuperSignal chemiluminescence(Pierce).

Injections into gut tube and embryo culture. Mouse E8.5 ICR embryos weredissected in Hanks Balanced Salt Solution and cultured in the DMEM/F12(Invitrogen) media supplemented with 50% rat serum (Valley Biomedical),penicillin, streptomycin, glutamine at 37° C. for 20-24 hrs. The YFPmouse ES cells were cultured in the presence of hit compounds for 6 daysto induce endoderm formation and then cells were dissociated withtrypsin and approx. 100 000 cells were injected into gut tube of E8.75embryos. Following injections, embryos were transferred to rotatingbottle culture unit and were then cultured in media (1.5-2 ml perembryo) as above under humidified conditions at 40% O₂, 5% CO₂, 55% N₂,and 37° C. After 30 hrs culture, embryos were fixed in 4%paraformaldehyde in PBS, embedded in tissue-tek and cryosections werestained with antibodies against Cld6, FoxA2 an YFP.

Example 1

Screening with ES Cells for Endoderm Formation

A screen of 4000 compounds was performed to search for cell permeablesmall molecules that direct differentiation of ES cells into theendodermal lineage. Two compounds were found to induce nearly 80% of EScells to form definitive endoderm, an efficiency higher than thatachieved with Activin A or Nodal, the two most commonly used proteininducers of endoderm. Chemically induced endoderm expresses multipleendodermal markers, can participate in normal development when injectedinto the embryonic gut tube and can also be differentiated intopancreatic progenitors in vitro. This protocol to differentiate mouseand human ES cells into definitive endoderm and pancreatic progenitorswith small molecules represents a step toward achieving a reproducibleand efficient production of desired ES cell derivatives.

Specifically, describe herein are two small molecules, IDE1 and IDE2(shown herein in FIG. 2A) that can efficiently induce definitiveendoderm (IDE) from mouse ES cells. Treatment of mouse ES cell monolayercultures with either compound yields high quantities of endodermexpressing multiple endodermal marker genes. Chemically derived endodermdevelops into pancreatic progenitors in vitro in response to the growthfactor FGF10, retinoic acid and hedgehog inhibitors, a commonly usedcombination to induce pancreatic progenitors in vitro. Moreover, the arecently identified small molecule, Indolactam V, was applied thatinduces pancreatic progenitors in human ES cell culture, to either IDE1or IDE2 derived endoderm, and induce higher yields of pancreaticprogenitors as compared to a growth factor based approach. Finally, itis demonstrated that compound induced endoderm can contribute to guttube formation in vivo when the cells are injected into the developinggut tube of mouse embryos. Two small molecules are introduced, whichinduce a robust differentiation of mouse ES cells into endoderm that hasthe same or a very similar developmental potential to its in vivocounterpart. The induction of endoderm from ES cells by IDE1 and IDE2 isconserved between mouse and human species.

To obtain a reporter for endoderm formation the inventors generated amouse ES cell line with the red-fluorescent protein dTomato, a variantof DsRed (Shaner et al., 2004) coding sequence under control of theSox17 promoter (FIG. 8A). Several lines of evidence show that Sox17 isan endodermal marker, both definitive and extra-embryonic. A nullmutation in mice is devoid of foregut endoderm and mid- and hindgutendoderm fails to expand (Kanai-Azuma et al., 2002). Gene expressionanalysis of isolated endoderm confirms that Sox17 is a marker ofendoderm, both definitive and extra-embryonic (Sherwood et al., 2007).However, Sox17 expression is not restricted exclusively to endoderm;genetic lineage tracing shows that Sox17 is expressed in the endodermallineage as early as E7.5 and but later on marks the gut tube as well asother organs (Park et al. 2006; Kim et al., 2007; Liu et al., 2007; R.Maehr, unpublished data).

In vitro, application of TGF-β family of growth factors, includingActivin A or Nodal, to both mouse and human ES cell cultures, leads tothe preferential differentiation into endodermal lineages (Kubo et al.,2004; Yasunaga et al., 2005; D'Amour et al., 2005). Consistent withthose previous studies, endoderm induction is observed when Sox17-dsRedmouse ES cells are treated with Activin A for 6 days in low serumconditions (see Methods). At 6 days, 45% of cells stain positively forSox17 and express dsRed (data not shown). All dsRed+ cells also expressSox17 protein as judged by Sox 17 antibody staining, which shows thatthe reporter line accurately reflects endogenous Sox17 expression. Theco-expression of the fluorescent marker and endogenous Sox17 was alsoconfirmed at all time points in vitro as well as in E6.5 and E7.5embryos (data not shown). There is a minor population of cells (10±3.6%)that stained for Sox17, but did not express dsRed; however, no falsepositive expression of the transgene (DsRed positive but Sox17 antibodynegative) was observed.

The endoderm differentiation protocol used in this screen is based onpreviously published protocols (Kubo et al., 2004; Yasunaga et al.,2005; D'Amour et al., 2005) with several modifications to allow endodermlineage induction in a high throughput format. Specifically, theinventors culture the mouse ES cells as a monolayer (in contrast toembryoid bodies) in gelatin-coated 384 well plates without any feedercell layer. The inventors also adjusted the cell density and mediacomposition to promote better survival of mouse ES cells (see Methodsfor details).

Twelve hours after plating, Sox17-dsRed mouse ES cells were suppliedwith differentiation media (low serum content) and a single chemicalcompound was added by pin transfer. At this time point, (x=0) no dsRed+and/or Sox17 antibody reactive cells were detected. In contrast, nearlyall cells expressed Oct4, a pluripotency marker (data not shown). Afterday 6 of culture in the presence of compounds, the inventors evaluatedSox17/DsRed expression and total cell number by flow cytometry.

Over 4,000 compounds were tested from a small molecule collectionconsisting of known compounds that influence stem cell fate (such asretinoic acid and 5-azacytidine), bioactive compounds, compounds withknown activity in signaling pathways, US Food and Drug Administrationapproved drugs, and a histone deacetylase (HDAC) inhibitors biased smallmolecule library resulting from diversity oriented synthesis.

Positive hits were defined as compounds that induce expression ofSox17/dsRed at three standard deviations above the DMSO (vehicle)control and were not auto-fluorescent or cytotoxic (FIG. 1B). Effects oncell viability or toxicity were set by requiring that the number ofcells after 6 days of culture doubled i.e. reaching at least 1600cells/well. Activin A treatment was used as a positive control. Theeffects of various treatments on differentiation were first evaluated byflow cytometric analysis for dsRed expressing cells and later confirmedby Sox17 and FoxA2 immunofluorescence and quantative-RT-PCR (Q-RT-PCR)analysis of endodermal markers including Sox/7, FoxA2, Gata4, Gata6,alpha-fetoprotein (Afp) and Sox7. Twenty seven compounds, ˜1.5% of totalscreened compounds, were selected as primary hits and furthercharacterized. The inventors also tested for the expression ofectodermal genes including Sox1, Pax6, Zic1 and mesodermal markersPdgfr-α; Pdgfr-β and Meoxl by Q-RT-PCR (data not shown) to ensurespecificity. Finally, since propensity to form different germ layer celltypes varies between different mouse and human ES cell lines (Burridgeet al., 2007; Osafune et al., 2008), the inventors tested primary hitsusing three mouse ES cell lines of two different genetic backgrounds(129 and 129/C57BL6 hybrid). Considering all these criteria, two smallmolecules, IDE1 and IDE2, were identified, out of the 27 primary hits,as inducers of endoderm and selected for further studies (FIG. 1B).

Example 2

Induction of Definitive and Extra-Embryonic Endoderm.

During evaluation of primary hit compounds, the inventors observed thatsmall molecules induced Sox17+ cells with two distinct morphologies. Oneclass, including IDE1 and IDE2, induced clustered populations of Sox17+cells, whereas other compounds led to the formation of a dispersedpopulation of Sox17+ cells. In particular, the Sox17+ cells induced byIDE2 or IDE1 form a compact, epithelial sheet as identified byimmunostaining with α-Sox17 antibody, whereas cells are more dispersedfollowing treatment with a different small molecule (XE09), one thatalso induces Sox17 expression (data not shown). A third class ofcompounds induced cells with a mixed morphology. Sox17 is expressed indefinitive endoderm, but also in extra-embryonic endoderm, and in othergerm layer derivatives at later stages of development including vascularendothelium (Kanai-Azuma et al., 2002; Matsui et al., 2006). Since thepositive identification of definitive endoderm is hindered by the lackof unique markers that are expressed exclusively there, and not presentin other types of endoderm, the inventors performed a negative selectionand tested for markers of extra-embryonic endoderm. It was found, thatthe vast majority (>95%) of the dispersed Sox17+ cells (class II) alsoexpressed extra-embryonic endoderm markers including Gata4 (Morrisey etal., 1996), SPARC (Mason et al., 1986), AFP (Dziadek, 1979) and Dab2(Yang et al., 2002) (Suppl. FIG. 2B). In particular, expression ofextra-embryonic endoderm markers (EE), such as GATA4, SPARC, AFP andDab2 are present in the dispersed population of Sox17+ cells but onlyrarely detected in the compact population of Sox17+ cells induced by theIDE2 compound. Similarly, treatment with IDE1 leads to marginalexpression of EE markers (data not shown). Conversely, Sox17+ cellsinduced by treatment with either IDE2 or IDE1 (data not shown) formedclustered, epithelial like populations and contained no or a negligiblenumber of cells positive for extra-embryonic markers.

Optimization of Definitive Endoderm Induction by Active Compounds

IDE1 and IDE2 are products of de novo chemical synthesis and come from alibrary of putative HDAC inhibitors (FIG. 2A, 2B). Titration of IDE1 andIDE2 from 50 nM to 5 μM showed that they function in a dose-dependentmanner (EC₅₀=125 nM for IDE1 and EC₅₀=223 nM for IDE2, FIG. 2B) with thehighest efficiency, and no toxicity, in the 250-800 nM range. Theoptimal concentration of IDE1 induces Sox17 expression in 80% and IDE2in 72% of total ES cells at day 6 of treatment (data not shown), whereαSox17 immunofluorescence was used to quantify the percent of totalcells expressing Sox17 induction in mouse ES cells by each compound atday 6 of treatment. The majority of Sox17+ cells (≧95%) induced by IDE1or IDE2 chemical treatment co-express another definitive endodermmarker, FoxA2. The inventors also tested for the expression of FoxA2(also known as HNF3β), as an essential gene for the development of thedefinitive endoderm in mouse, (Ang et al., 1993; Monaghan et al., 1993;Sasaki and Hogan, 1993) and observed that over 95% of IDE1 or IDE2compound induced Sox17+ cells co-express FoxA2 (data not shown).

Time Course and Synergy Between Active Compound and Growth Factors.

Endoderm induction peaks at day 6 of treatment with small molecules,when 81±14% (for IDE1) treatment and 76±14% (for IDE2) out of total cellnumber were Sox17+ (FIGS. 3A, 3B and 3C). In the course of the next 8days, the efficiency of endodermal induction does not significantlychange. Compared to Activin A treatment both small molecules, under theconditions reported here, induced more cells to express Sox17, and atearlier time points. The percentage of cells expressing Sox17 at day 2of treatment is 34% for IDE1 (FIG. 3A) and 32% for IDE2 (FIG. 3B),whereas Activin A yielded 13% Sox17+ cells (FIG. 3C); at day 4, 40-50%of cells treated with either of the compounds are Sox17+, whereas only28% of Activin A treated cells are Sox17+.

Simultaneous treatment of mouse ES cells with both IDE1 and IDE2 did notproduce any synergistic effect on Sox17+ induction (FIG. 3D).Co-treatment with IDE2 and Nodal, significantly (p≦0.001) increases theSox17 induction at day 4 to 55.8±6.49%, compared to 42±3.83% with thecompound alone. Wnt3a has no significant effect on Sox17 expression whencombined with compounds.

IDE1 and IDE2 Induce Endoderm from Human Embryonic Stem Cells

The inventors also tested whether the hit compounds, have the ability todirect also human ES cells (HUES) into endodermal fate. Two HUES lines,HUES 4 and 8, treated with IDE1 and IDE2 compounds show propensity todifferentiate into endodermal lineage (Osafune, 2008) and judged bySox17 expression. Both compounds induced Sox17 expression indose-depended manner. Treatment with IDE1 (100 nM) for 4 days leads toSox17 expression in 62±8.1% of cells, an efficiency similar to Activin Atreatment in these culture condition (64±6.3%). IDE2 (200 nM) inducesSox17 expression in 57±6.7% of total cell number, (data not shown) andthe effect of IDE2 is significant different (p=0.00255) compared to themock treatment (16%±3.6). Human ESC cultures were treated for 6 dayswith Activin A or vehicle (DMSO) only. Activin A treatment leads toSox17 expression in 55-65% of total cells, which is 4-fold increase ascompared to the vehicle treatment (data not shown). Co-treatment ofhuman ES cells with Activin A and Wnt3a increases the efficiency ofendoderm induction only by an additional 3-5%. A similar efficiency ofendoderm induction was observed when HUES were culture in presence ofMEF layer or on gelatin coated plates.

Example 3

Gene Expression Analysis of Endoderm Induced by Active Compounds

To determine whether other genes that compose part of an endodermalsignature are induced in mouse ES cell cultures treated with activecompounds, Sox17-DsRed+ cells were isolated by flow cytometry after day6 of compound stimulation and profiled by gene expression analysis. Ofnineteen genes previously defined as a definitive endoderm signature inthe mouse (Sherwood et al., 2007), fourteen were induced more than twofold in the compound treated samples compared to mock treatment (FIG.4A). Also compared was in vitro derived endoderm with its in vivocounterparts sorted-out from Sox17-DsRed E7.5-E8.5 embryos. Of thesenineteen endoderm signature genes, only two genes, Spink3 and Tmprss2,were significantly different and were expressed at higher levels in theE7.5 endoderm (FIG. 4A). Furthermore, no significant changes in theexpression of markers characteristic for other cell lineages wereobserved, such as the ectoderm markers Zic1, Pax6, and mesoderm markersFlk1, CD31 (data not shown) after compound treatment. The r² value(square of linear correlation coefficient) between chemically inducedendoderm and Sox17/dsRed+ endoderm isolated from mouse E7.5-E8.0 embryoswas 0.94-0.97 in three independent experiments (FIG. 4B). In contrast,the r² value for non-treated mouse ES cells and naïve endoderm isolatedform E.75-8.0 embryos was 0.5-0.56 (FIG. 4B). These data suggest that invitro derived endoderm by hit compound treatment is essentiallyequivalent to E7.5-E8.0 endoderm with respect to the expression of keyendodermal markers.

Activation of Nodal/Smad Signaling in Sox17+ Cells Produced by SmallMolecules IDE1 and IDE2 Treatment

Genetic and biochemical studies point to Smad proteins as theintracellular transducers of TGF-β signaling, including Activin A andNodal (Whitman, 1998) and a high level of Smad2 phosphorylation isdetected in cells lysates of ES cells that have been treated withActivin A or Nodal treatment. Both IDE1 and IDE2 induce phosphorylationof Smad2 after 24 hrs or longer at levels comparable to that induced byActivin A treatment (FIG. 5A). This phosphorylation of Smad2 is stronglyattenuated by co-treatment of mouse ES cells with either of IDE1 or IDE2compounds and the Activin receptor-like kinase 4/5/7 (ALK) inhibitor,SB43125. Under these conditions, induction of Sox17 protein is alsoreduced to 5.6±1.3% (data not shown). These data indicate that both IDE1and IDE2 function by activating the TGF□ signaling pathway, however thespecific biochemical targets of these small molecules are unknown.

Treatment with either of IDE1 or IDE2 compounds for 6 hrs leads toupregulation of Nodal transcripts by 6-8-fold compared to the control(FIG. 5B) and the levels of Nodal expression increase further with timeof compound exposure. Nodal treatment increases its own expression atsimilar levels and time schedule. This may reflect an autoregulatorymechanism for maintaining and upregulating Nodal expression through aSmad2/FAST-1-dependent autoregulatory loop that feeds on Nodaltranscription (Agius et al., 2000; Pogoda et al., 2000).

Example 4

In Vivo Competency of Chemically Derived Endoderm

For chemically derived endoderm to be useful, it is important todetermine its developmental potential, beyond the expression ofendodermal markers. The ultimate goal is to direct the cells to formfunctional beta cells. To begin to address this possibility andfunctional potential of derived populations, mouse ES cells ubiquitouslyexpressing enhanced yellow fluorescent protein (EYFP) (Hadjantonakis etal., 2002) were induced to form endoderm with IDE1, IDE2, or DMSO(control). At day 6 of treatment, the inventors dissociated and injectedthe cells into the gut tube (a derivative of endoderm) of live E8.75embryos. The lumen of the gut tube can be accessed prior to thecompletion of embryonic turning and gut tube closure and thereforeprovides a developmental window for functional assessment of ES-derivedendoderm cells. Chemically derived endoderm was injected into theprimitive gut tube at the anterior and posterior intestinal portals. Atthis time the gut tube is still open and anterior intestinal portal isaccessible (FIG. 6A). The embryos were cultured ex vivo for 24-30 hrsduring which time the lateral walls of the embryonic gut fold ventrallyand the gut tube closes, around E9.5. ES derived endodermal cellsinduced by small molecules integrated into the developing gut tube,whereas control treated ES cells did not. Moreover, ES cell derivedendoderm showed the characteristic morphology of gut cells and expressedmarkers of gut tube markers including FoxA2 and Claudin6 (Anderson etal., 2008) (FIG. 6B). Cells induced by IDE1 treatment integrated intothe gut, in 8 out of 35 cases, and in 7 out of 29 embryos for IDE2.Conversely, DMSO (control) treated cells never integrate into thedeveloping gut tube (0/10 and 0/11, respectively) and instead remain inthe lumen (FIG. 6B).

In Vitro Potential of Compound Induced Endoderm

To further evaluate the developmental potential of compound inducedendoderm, the inventors tested whether it can differentiate in vitrointo pancreatic progenitors. Pancreatic progenitors appear in thepancreatic bud at E9.5 and are marked by the expression of thetranscription factor Pdx1. Pdx1 is required for pancreas development andβ-cell formation, as a null mutation of Pdx1 in mice results in afailure to form a pancreas (Jonsson et al., 1994; Offield et al., 1996)and lineage tracing studies show that Pdx1 marks progenitors that giverise to all pancreatic cell types (Gu et al., 2003). Using Pdx1-GFPknock-in (Micallef et al., 2005) mouse ES cells the inventors induceddefinitive endoderm using either of the hit compounds and cultured cellsin various conditions for additional six days.

Published protocols for differentiation of ES cells into pancreaticprogenitors are based on studies of the factors that modulate signalingduring pancreatic organogenesis (Stafford and Prince, 2002; Lau et al.,2006; Bhushan et al., 2001). For example, in one protocol, endoderm isinduced with Activin A, followed by treatment with FGF10 and theHedgehog signaling inhibitor KAAD-cyclopamine for 3 days, and thenexposed to a posteriorizing factor, retinoic acid, for an additional 3days to induce Pdx1 expression (D'Amour et al., 2006). Using thisregimen, 12.1±4% of the mouse ES cells differentiate further intopancreatic progenitors, defined by Pdx1+ expression. By comparison, whencompound induced endoderm was used as a starting population, instead ofActivin A induced endoderm, 25±6% of cells expressed Pdx1. Spontaneousdifferentiation, in the absence of hit compounds, additional growthfactors or signaling modulators, occurs at a lower level, producing GFPexpression in 4.6±1.1% of cells (FIG. 7).

Example 5

Indolactam V can Induce Pancreatic Progenitors from Human Endoderm Cells

The inventors also performed a separate chemical screen using humancells to identify a compound, Indolactam V, that can induce pancreaticprogenitors from endoderm that has been produced from human ES cells.Indolactam V is also able to efficiently induce pancreatic progenitors(Pdx1+ cells) in endoderm derived by chemical treatment of human ormouse ES.

Treatment of IDE1 or IDE2 induced mouse endoderm yields 51±7.4% Pdx1-GFPexpressing pancreatic progenitors at day 6 (FIG. 7). In particular,endoderm enriched cultures were grown for another 6 days in chemicallydefined media containing: DMSO without any additional growth factors orIDE1 or IDE2 compounds (control), in presence of growth factors (FGF10,CYC, RA) or in the presence of Indolactam V (ILV) to induce theexpression of Pdx1. At day 12, in cultures treated initially with IDE1or IDE2 and followed by ILV, 50% of the total cells were Pdx1+, a10-fold increase above control treatment (data not shown). When cultureswere stained with Pdx1 antibodies similar number (53±6.4%) of positivecells were observed after two-step treatment with small molecules,namely a first step of culturing in the presence of IDE1 and/or IDE2,then a second stem of culturing in the presence of Indolactam V (ILV).Notably, this is a 10-fold increase in Pdx1+ cell number compared to thecontrol DMSO treated and a 4-fold increase compared to known publishedprotocols. The majority of Pdx1+ (92±5%) cells also express otherpancreatic progenitor markers, including HNF6. For example, coexpressionof pancreatic markers, Pdx1 and HFN6 was detected by immunostaining incells induced by a two-step small molecule protocol; where the firststep comprises contacting the mouse ESCs with IDE2 or IDE1 for about 6days to induce definitive endoderm and then, in the second step, wherethe IDE1 or IDE2-induced definitive endoderm cells were treated withIndolactam V for an additional 6 days to allow pancreatic progenitorspecification, which were detected using antibodies co-expressing bothPdx1 and HNF6 (data not shown). Together, these compounds provide atwo-step protocol for in vitro generation of pancreatic progenitors thatutilizes the small molecules at each step, first as inducers of endodermand later to generate pancreatic progenitors.

Described herein are two potent small molecules, IDE1 and IDE2 that candirect mouse ES cells differentiation such that 70-80% of cells areendoderm cells. Both compounds are products of de novo synthesis andtheir biological activity has not been previously reported. Thisefficiency of induction compares favorably with published protocolsemploying TGF-β family members, e.g. Activin A or Nodal, which produceabout 45% endoderm. Both IDEs small molecules induce endoderm formationin human ES cell cultures. In the long term, the potential benefits offinding chemicals like IDE1 or IDE2 include the prospect of minimizingthe risk of animal disease infections and a cost reduction for materialsand the temporal control that can be achieved using small moleculeswhich can be easily delivered and removed. Application of either of thetwo small molecules reported here does not eliminate the necessity ofserum presence in the differentiation protocols. These results enhancethe repertoire of chemical compounds for manipulating ES cell fate andencourage the high throughput screening of small molecules to directdifferentiation of ES cells under chemically defined conditions.

With respect to their potential to induce endoderm, IDE1 and IDE2 appearto be interchangeable as substantial differences as far as efficiency,gene expression or functional potential between populations induced bythe two compounds was observed. Both compounds are novel and theirspecific biological targets remain to be identified, but a strong hintcomes from the fact that they activate part of a TGF-β pathway asevidenced by Smad2 phosphorylation.

In the experiments reported here, mouse ES were cultured in the absenceof feeders or other supportive cell types. However, extrinsic signalingcould well improve the efficiency of the differentiation and maturationof cells. Interactions between endoderm and different mesodermal celltypes pattern the gut epithelium into progenitor domains and promotelocal organ outgrowth (Horb and Slack, 2001; Deutsch et al., 2001; Kumaret al., 2003). One source for prospective inductive signals ispancreatic mesenchyme which supports budding of dorsal pancreatic tissueinto the stroma (Golosow and Grobstein, 1962; Wells and Melton, 2000).Another important signal comes from vessel endothelium which providesinductive signals for islet development (Lammert et al., 2001). Futurestudies may identify small molecule substitutes for these developmentalsignals.

If in vitro differentiation of ES cells is to be used for treating humandiseases, including diabetes, it will likely require derivation of largequantities of cells with high purity in chemically defined conditions.This study shows the feasibility of chemical screening to identifymolecules that may achieve this effect, in this case direct ES cellsinto endoderm, which is relevant for liver, lung, stomach, intestine,and thymus as well as the pancreas.

Although certain aspects, examples and embodiments have been describedabove, it will be recognized by the person of ordinary skill in the art,given the benefit of this disclosure, that additions, substitutions,modifications, and alterations of the disclosed illustrative aspects,examples and embodiments are possible.

REFERENCES

All references cited herein are incorporated herein by reference intheir entirety as if each individual publication or patent or patentapplication was specifically and individually indicated to beincorporated by reference in its entirety.

-   Agius, E., Oelgeschlager, M., Wessely, O., Kemp, C., and De    Robertis, E. M. (2000). Endodermal Nodal-related signals and    mesoderm induction in Xenopus. Development 127, 1173-1183.-   Anderson, W. J., Zhou, Q., Alcalde, V., Kaneko, O. F., Blank, L. J.,    Sherwood, R. I., Guseh, J. S., Rajagopal, J., and Melton, D. A.    (2008). Genetic targeting of the endoderm with claudin-6(CreER). Dev    Dyn 237, 504-512.-   Ang, S. L., Wierda, A., Wong, D., Stevens, K. A., Cascio, S.,    Rossant, J., and Zaret, K. S. (1993). The formation and maintenance    of the definitive endoderm lineage in the mouse: involvement of    HNF3/forkhead proteins. Development 119, 1301-1315.-   Bhushan, A., Itoh, N., Kato, S., Thiery, J. P., Czernichow, P.,    Bellusci, S., and Scharfmann, R. (2001). Fgf10 is essential for    maintaining the proliferative capacity of epithelial progenitor    cells during early pancreatic organogenesis. Development 128,    5109-5117.-   Burridge, P. W., Anderson, D., Priddle, H., Barbadillo Munoz, M. D.,    Chamberlain, S., Allegrucci, C., Young, L. E., and Denning, C.    (2007). Improved human embryonic stem cell embryoid body homogeneity    and cardiomyocyte differentiation from a novel V-96 plate    aggregation system highlights interline variability. Stem Cells 25,    929-938.-   Chen, S., Do, J. T., Zhang, Q., Yao, S., Yan, F., Peters, E. C.,    Scholer, H. R., Schultz, P. G., and Ding, S. (2006). Self-renewal of    embryonic stem cells by a small molecule. Proc Natl Acad Sci USA    103, 17266-17271.-   D'Amour, K. A., Agulnick, A. D., Eliazer, S., Kelly, O. G., Kroon,    E., and Baetge, E. E. (2005). Efficient differentiation of human    embryonic stem cells to definitive endoderm. Nat Biotechnol 23,    1534-1541.-   D'Amour, K. A., Bang, A. G., Eliazer, S., Kelly, O. G., Agulnick, A.    D., Smart, N. G., Moorman, M. A., Kroon, E., Carpenter, M. K., and    Baetge, E. E. (2006). Production of pancreatic hormone-expressing    endocrine cells from human embryonic stem cells. Nat Biotechnol 24,    1392-1401.-   Desbordes, S.C., Placantonakis, D. G., Ciro, A., Socci, N. D., Lee,    G., Djaballah, H., and Studer, L. (2008). High-throughput screening    assay for the identification of compounds regulating self-renewal    and differentiation in human embryonic stem cells. Cell Stem Cell 2,    602-612.-   Deutsch, G., Jung, J., Zheng, M., Lora, J., and Zaret, K. S. (2001).    A bipotential precursor population for pancreas and liver within the    embryonic endoderm. Development 128, 871-881.-   Diamandis, P., Wildenhain, J., Clarke, I. D., Sacher, A. G., Graham,    J., Bellows, D. S., Ling, E. K., Ward, R. J., Jamieson, L. G.,    Tyers, M., and Dirks, P. B. (2007). Chemical genetics reveals a    complex functional ground state of neural stem cells. Nat Chem Biol    3, 268-273.-   Ding, S., and Schultz, P. G. (2004). A role for chemistry in stem    cell biology. Nat Biotechnol 22, 833-840.-   Dziadek, M. (1979). Cell differentiation in isolated inner cell    masses of mouse blastocysts in vitro: onset of specific gene    expression. J Embryol Exp Morphol 53, 367-379.-   Golosow, N., and Grobstein, C. (1962). Epitheliomesenchymal    interaction in pancreatic morphogenesis. Dev Biol 4, 242-255.

Gu, G., Brown, J. R., and Melton, D. A. (2003). Direct lineage tracingreveals the ontogeny of pancreatic cell fates during mouseembryogenesis. Mech Dev 120, 35-43.

-   Hadjantonakis, A. K., Macmaster, S., and Nagy, A. (2002). Embryonic    stem cells and mice expressing different GFP variants for multiple    non-invasive reporter usage within a single animal. BMC Biotechnol    2, 11.-   Horb, M. E., and Slack, J. M. (2001). Endoderm specification and    differentiation in Xenopus embryos. Dev Biol 236, 330-343.-   Jonsson, J., Carlsson, L., Edlund, T., and Edlund, H. (1994).    Insulin-promoter-factor 1 is required for pancreas development in    mice. Nature 371, 606-609.-   Kanai-Azuma, M., Kanai, Y., Gad, J. M., Tajima, Y., Taya, C.,    Kurohmaru, M., Sanai, Y., Yonekawa, H., Yazaki, K., Tam, P. P., and    Hayashi, Y. (2002). Depletion of definitive gut endoderm in    Sox17-null mutant mice. Development 129, 2367-2379.-   Kim, I., Saunders, T. L., and Morrison, S. J. (2007). Sox17    dependence distinguishes the transcriptional regulation of fetal    from adult hematopoietic stem cells. Cell 130, 470-483.-   Kubo, A., Shinozaki, K., Shannon, J. M., Kouskoff, V., Kennedy, M.,    Woo, S., Fehling, H. J., and Keller, G. (2004). Development of    definitive endoderm from embryonic stem cells in culture.    Development 131, 1651-1662.-   Kumar, M., Jordan, N., Melton, D., and Grapin-Botton, A. (2003).    Signals from lateral plate mesoderm instruct endoderm toward a    pancreatic fate. Dev Biol 259, 109-122.-   Lammert, E., Cleaver, O., and Melton, D. (2001). Induction of    pancreatic differentiation by signals from blood vessels. Science    294, 564-567.-   Lau, J., Kawahira, H., and Hebrok, M. (2006). Hedgehog signaling in    pancreas development and disease. Cell Mol Life Sci 63, 642-652.-   Lewis, S. L., and Tam, P. P. (2006). Definitive endoderm of the    mouse embryo: formation, cell fates, and morphogenetic function. Dev    Dyn 235, 2315-2329.-   Liu, Y., Asakura, M., Inoue, H., Nakamura, T., Sano, M., Niu, Z.,    Chen, M., Schwartz, R. J., and Schneider, M. D. (2007). Sox17 is    essential for the specification of cardiac mesoderm in embryonic    stem cells. Proc Natl Acad Sci USA 104, 3859-3864.-   Mason, I. J., Murphy, D., Munke, M., Francke, U., Elliott, R. W.,    and Hogan, B. L. (1986). Developmental and transformation-sensitive    expression of the Sparc gene on mouse chromosome 11. Embo J 5,    1831-1837.-   Matsui, T., Kanai-Azuma, M., Hara, K., Matoba, S., Hiramatsu, R.,    Kawakami, H., Kurohmaru, M., Koopman, P., and Kanai, Y. (2006).    Redundant roles of Sox17 and Sox18 in postnatal angiogenesis in    mice. J Cell Sci 119, 3513-3526.-   McLean, A. B., D'Amour, K. A., Jones, K. L., Krishnamoorthy, M.,    Kulik, M. J., Reynolds, D. M., Sheppard, A. M., Liu, H., Xu, Y.,    Baetge, E. E., and Dalton, S. (2007). Activin a efficiently    specifies definitive endoderm from human embryonic stem cells only    when phosphatidylinositol 3-kinase signaling is suppressed. Stem    Cells 25, 29-38.-   Micallef, S. J., Janes, M. E., Knezevic, K., Davis, R. P.,    Elefanty, A. G., and Stanley, E. G. (2005). Retinoic acid induces    Pdx1-positive endoderm in differentiating mouse embryonic stem    cells. Diabetes 54, 301-305.-   Monaghan, A. P., Kaestner, K. H., Grau, E., and Schutz, G. (1993).    Postimplantation expression patterns indicate a role for the mouse    forkhead/HNF-3 alpha, beta and gamma genes in determination of the    definitive endoderm, chordamesoderm and neuroectoderm. Development    119, 567-578.-   Morrisey, E. E., Ip, H. S., Lu, M. M., and Parmacek, M. S. (1996).    GATA-6: a zinc finger transcription factor that is expressed in    multiple cell lineages derived from lateral mesoderm. Dev Biol 177,    309-322.-   Offield, M. F., Jetton, T. L., Labosky, P. A., Ray, M., Stein, R.    W., Magnuson, M. A., Hogan, B. L., and Wright, C. V. (1996). PDX1-1    is required for pancreatic outgrowth and differentiation of the    rostral duodenum. Development 122, 983-995.-   Osafune, K., Caron, L., Borowiak, M., Martinez, R. J.,    Fitz-Gerald, C. S., Sato, Y., Cowan, C. A., Chien, K. R., and    Melton, D. A. (2008). Marked differences in differentiation    propensity among human embryonic stem cell lines. Nat Biotechnol 26,    313-315.-   Park, K. S., Wells, J. M., Zorn, A. M., Wert, S. E., and    Whitsett, J. A. (2006). Sox17 influences the differentiation of    respiratory epithelial cells. Dev Biol 294, 192-202.-   Pogoda, H. M., Solnica-Krezel, L., Driever, W., and Meyer, D.    (2000). The zebrafish forkhead transcription factor FoxH1/Fast1 is a    modulator of nodal signaling required for organizer formation. Curr    Biol 10, 1041-1049.-   Sakamoto, Y., Hara, K., Kanai-Azuma, M., Matsui, T., Miura, Y.,    Tsunekawa, N., Kurohmaru, M., Saijoh, Y., Koopman, P., and Kanai, Y.    (2007). Redundant roles of Sox17 and Sox18 in early cardiovascular    development of mouse embryos. Biochem Biophys Res Commun 360,    539-544.-   Sasaki, H., and Hogan, B. L. (1993). Differential expression of    multiple fork head related genes during gastrulation and axial    pattern formation in the mouse embryo. Development 118, 47-59.-   Shaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N.,    Palmer, A. E., and Tsien, R. Y. (2004). Improved monomeric red,    orange and yellow fluorescent proteins derived from Discosoma sp.    red fluorescent protein. Nat Biotechnol 22, 1567-1572.-   Sherwood, R. I., Jitianu, C., Cleaver, O., Shaywitz, D. A.,    Lamenzo, J. O., Chen, A. E., Golub, T. R., and Melton, D. A. (2007).    Prospective isolation and global gene expression analysis of    definitive and visceral endoderm. Dev Biol 304, 541-555.-   Stafford, D., and Prince, V. E. (2002). Retinoic acid signaling is    required for a critical early step in zebrafish pancreatic    development. Curr Biol 12, 1215-1220.-   Wells, J. M., and Melton, D. A. (1999). Vertebrate endoderm    development. Annu Rev Cell Dev Biol 15, 393-410.-   Wells, J. M., and Melton, D. A. (2000). Early mouse endoderm is    patterned by soluble factors from adjacent germ layers. Development    127, 1563-1572.-   Whitman, M. (1998). Smads and early developmental signaling by the    TGFbeta superfamily. Genes Dev 12, 2445-2462.-   Wu, X., Ding, S., Ding, Q., Gray, N. S., and Schultz, P. G. (2004).    Small molecules that induce cardiomyogenesis in embryonic stem    cells. J Am Chem Soc 126, 1590-1591.-   Yang, D. H., Smith, E. R., Roland, I. H., Sheng, Z., He, J.,    Martin, W. D., Hamilton, T. C., Lambeth, J. D., and Xu, X. X.    (2002). Disabled-2 is essential for endodermal cell positioning and    structure formation during mouse embryogenesis. Dev Biol 251, 27-44.-   Yasunaga, M., Tada, S., Torikai-Nishikawa, S., Nakano, Y., Okada,    M., Jakt, L. M., Nishikawa, S., Chiba, T., and Era, T. (2005).    Induction and monitoring of definitive and visceral endoderm    differentiation of mouse ES cells. Nat Biotechnol 23, 1542-1550.

What is claimed is:
 1. A method of producing a definitive endoderm cellfrom a pluripotent stem cell comprising contacting a population ofpluripotent stem cells with at least one compound of Formula (I) thatactivates TGF-β signaling, thereby inducing the differentiation of atleast one pluripotent stem cell into a definitive endoderm cell, whereinthe definitive endoderm cell expresses Sox17, or HNF3B (FoxA2), or Sox17and HNF3B (FoxA2) and wherein the compound of formula (I) is:

wherein: R¹ and R² are independently H, alkyl, alkenyl, alkynyl, aryl,heteroaryl, cyclyl, or cyclyl, each of which can be optionallysubstituted and/or can be interrupted in the backbone with one or moreof O, N, S, S(O), and C(O); R³ and R⁴ are independently H, halogen,alkyl, alkenyl, alkynyl, alkoxy, aryl, heteroaryl, cyclyl, or cyclyl,each of which can be optionally substituted, or R³ and R⁴ together withthe carbon to which they are attached from an optionally substitutedcyclyl or heterocyclyl; and L is C₁-C₁₀ alkylenyl, C₂-C₁₀ alkenylenyl,or C₂-C₁₀ alkynylenyl, each of which can be optionally substitutedand/or can be interrupted in the backbone with one or more of O, N, S,S(O), and C(O).
 2. The method of claim 1, wherein the pluripotent stemcell is an embryonic stem (ES) cell or an induced pluripotent stem (iPS)cell.
 3. The method of claim 1, wherein the stem cell is from a mammal.4. The method of claim 1, wherein the stem cell is a human stem cell. 5.The method of claim 1, wherein the method further comprising isolating apopulation of definitive endoderm cells, wherein at least 5%, 10%, 15%,20%, 25%, 30%, 35%, 50%, or 75% of the total cells in the isolatedpopulation are definitive endoderm cells.
 6. The method of claim 1,wherein the compound of formula (I) is2-[(6-carboxy-hexanoyl)-hydrazonomethyl]-benzoic acid (IDE1) or7-(2-cyclopentylidenehydrazino)-7-oxoheptanoic acid (IDE2).
 7. Themethod of claim 1, wherein the compound of formula (I) has the structure


8. The method of claim 1, the method further comprising exposing thestem cells to at least one additional agent.
 9. The method of claim 8,wherein the additional agent is selected from the group consisting of:Nodal, Activin A or Wnt3a.